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[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
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=== Cryo-EM Structure of the Human TRPV1 Ion Channel ===
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<table width="95%" border="0"><tr><td>
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{| align="left"
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<imagemap>
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Image:Cell press logo.png|300 px|
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default [http://cell.com]
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</imagemap>
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|}
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</td></tr><tr><td>
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<span style="font-size:160%"><b>Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.</b></span>
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<StructureSection
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</td></tr><tr><td>
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load='3j5p'
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size='340'
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side='right'
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caption='Cryo-EM structure of the human TRPV1 ion channel in the apo state (Liao et al., 2013; ~3.5 Å resolution)'
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scene=''>
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</StructureSection>
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=== Introduction ===
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<span style="font-size:120%">
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The transient receptor potential vanilloid 1 (TRPV1) ion channel is a heat- and ligand-gated cation channel essential for nociception, inflammatory pain, and thermal sensitivity. Activated by capsaicin, protons, noxious heat (>42°C), and lipid mediators, TRPV1 serves as a polymodal molecular sensor in the peripheral nervous system. Because of its central role in pain signaling, TRPV1 has been a major therapeutic target for developing next-generation analgesics. Understanding its three-dimensional structure is therefore crucial for elucidating its gating mechanism and ligand recognition.
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Hyung-Min Jeon, Jisung Eun, Kelly H. Kim, and Youngjin Kim.
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Cell Volume 33, Issue 11, P1856-1866.E5, November 06, 2025
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=== Structural Highlights ===
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https://doi.org/10.1016/j.str.2025.07.019
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Using single-particle cryo-electron microscopy, Liao, Cao, Julius, and Cheng (2013) determined the first near-atomic structures of TRPV1 in multiple functional states, including the apo (resting), capsaicin-bound, and toxin-bound conformations. TRPV1 assembles as a homotetramer, with each subunit containing six transmembrane helices (S1–S6), a re-entrant pore loop, and extensive cytosolic ankyrin repeat domains.
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</span>
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</td></tr></table>
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==Structure Tour==
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The vanilloid-binding pocket—formed between the S3–S4 helices and the S4–S5 linker—was resolved in detail, explaining how capsaicin stabilizes the open conformation by pulling on the S4–S5 linker and reshaping the S6 helices to widen the pore. Structures bound to the double-knot toxin (DkTx) reveal an even more dilated pore, representing a fully activated gating state. Comparisons across these states demonstrate the sequence of conformational rearrangements that underlie heat and ligand gating in TRPV1.
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<StructureSection load='9kkk' size='340' side='right'caption='Cryo-EM structure of human SLC22A6 (OAT1) in the apo-state, [[Resolution|resolution]] 3.85&Aring;' scene=''>
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===Background===
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Members of the organic anion transporter (OAT) family, including
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=== Significance ===
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OAT1, are expressed on the epithelial membrane of the kidney,
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liver, brain, intestine, and placenta. OAT1 regulates the transport
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of organic anion drugs from the blood into kidney epithelial
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cells by utilizing the α-ketoglutarate (α-KG) gradient across the
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membrane established by the tricarboxylic acid (TCA) cycle.The organic anion transporter 1 (OAT1) also plays a key role in excreting waste from organic drug metabolism and
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contributes significantly to drug-drug interactions and drug disposition. However, the structural basis of specific
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substrate and inhibitor transport by human OAT1 (hOAT1) has remained elusive. Here are four
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[[cryo-electron microscopy]] (cryo-EM) structures of hOAT1 in its inward-facing conformation: the apo
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form, the substrate (olmesartan)-bound form with different anions, and the inhibitor (probenecid)-bound
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form.
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===Cryo-EM structure of hOAT1===
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These cryo-EM structures provide a mechanistic blueprint for understanding how TRPV1 integrates thermal, chemical, and lipid-derived signals to regulate ion permeation. They reveal conserved gating transitions and define pharmacologically relevant ligand-binding pockets essential for rational drug design. The ability to visualize TRPV1 in distinct activation states enables development of selective analgesic modulators targeting neuropathic and inflammatory pain while minimizing adverse thermo-sensory effects.
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<center>{{Template:Green links zoom}}</center>
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Human
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=== References ===
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OAT1 adopts an inward-facing conformation in a membrane. OAT1 consist of structural features
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* Liao M., Cao E., Julius D., Cheng Y. (2013). Structure of the TRPV1 ion channel determined by electron cryo-microscopy. *Nature*, 504, 107–112.
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including intracellular helices domain (ICD),
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extracellular domain (ECD), N-lobe helices
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(TM1-6), and C-lobe helices (TM7-12). (right) The
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border of the binding cavity (described in solvent
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exclude-surface) is formed by residues N35,
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Y230, Y353, Y354 (upper), and M207 and F442
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(lower).
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'''Key Structural Characteristics:'''
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*'''Overall Fold:'''
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::*Adopts the classic Major Facilitator Superfamily (MFS) fold.
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::*Comprises 12 transmembrane helices (TMs 1-12).
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::*Exhibits pseudo-two-fold symmetry, divided into an N-lobe (TMs 1-6) and a C-lobe (TMs 7-12).
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*'''Central Binding Cavity:'''
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::*The cavity is located between the N-lobe (formed by TM1, TM2, TM4, TM5) and the C-lobe (formed by TM7, TM8, TM10, TM11).
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::*It possesses a positively charged electrostatic environment, which explains its strong preference for transporting anionic substrates.
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::*The cavity is lined by 29 residues, forming a hydrophobic and aromatic-rich environment.
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*'''Cavity Borders and Cytosolic Gate:'''
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::*The top border (extracellular side) of the cavity is formed by residues including N35, Y230, Y353, and Y354.
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::*The bottom border (cytosolic side) features a narrow "thin bottom gate" formed by residues M207 and F442. The interaction between these two residues splits the cytosolic entrance into two distinct pathways:
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:::*Path A: Located between TM2 and TM11.
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:::*Path B: Located between TM5 and TM8.
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*'''Conformational State:'''
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::*In the apo state, the transporter is in a relaxed, inward-open conformation, providing access for substrates from the cytoplasm.
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::*The structure serves as a baseline for understanding the conformational changes that occur upon substrate or inhibitor binding.
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===Olmesartan recognition by hOAT1===
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The structural and functional analysis of hOAT1 in complex with the high-affinity antihypertensive drug olmesartan provides a detailed blueprint for substrate specificity and binding.
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'''1. Binding Location and Pose'''
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:*Olmesartan binds within the central cavity of hOAT1 in an inward-facing conformation.
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:*It occupies Site 3 of the binding pocket, which is the primary polyspecific site for anionic substrates.
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:*The drug adopts a diagonal orientation relative to the membrane plane, a pose that requires more space than the smaller inhibitor probenecid. This orientation is similar to its conformation when bound to the angiotensin receptor.
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'''2. Key Interacting Residues'''
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Olmesartan is surrounded by residues from multiple transmembrane helices (TM1, TM4, TM5, TM7, TM10, TM11) within a 5 Å distance. The critical interactions involve:
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*'''Aromatic and Hydrophobic Cage:'''
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::*The biphenyl group of olmesartan is nestled near residue F438.
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::*The tetrazole ring is positioned between the bottom-gate residues M207 and F442.
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::*The imidazole moiety is located close to Y354.
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*'''Critical Role of Y230:'''
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::*Upon olmesartan binding, the side chain of Y230 undergoes a vertical rotation to accommodate and interact with the substrate.
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::*Mutagenesis studies confirm its importance: the Y230F mutation increased the IC₅₀ for olmesartan inhibition from 845.3 nM (Wild Type) to 2.36 µM, indicating a reduction in binding affinity.
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*'''The Bottom Gate Residues (M207 and F442):'''
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::*These residues are crucial for high-affinity olmesartan binding.
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::*The M207A mutant caused a 4-fold reduction in affinity (IC₅₀ = 3.78 µM).
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::*The F442A mutant caused a dramatic 12-fold reduction in affinity (IC₅₀ = 10.32 µM).
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::*This suggests these residues not only form a gate but also directly interact with large, transportable substrates like olmesartan.
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'''3. Chloride Ion Coordination is Essential'''
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A key finding is the role of a chloride ion in stabilizing the olmesartan-bound state.
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:*'''The Chloride-Binding Site:''' A chloride ion (or bromide, used for confirmation) is observed coordinated between residues S203, Y230, and R466.
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:*'''Indirect Role of S203:''' While S203 does not directly contact olmesartan, it is critical for chloride coordination. This is a major species-specific difference, as rat OAT1 has an alanine at this position.
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:*'''Functional Evidence of Chloride Dependence:'''
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::*The IC₅₀ of olmesartan is 2.01 µM in chloride-rich conditions but improves to 0.91 µM in chloride-depleted conditions, suggesting a more complex relationship where chloride may facilitate transport.
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::*The S203A mutant shows a severe ~5-fold reduction in olmesartan binding affinity specifically in the presence of chloride (IC₅₀: WT = 2.47 µM; S203A = 29.52 µM).
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::*The S203A-Y230F double mutant has an even more profound effect, increasing the IC₅₀ to 93.30 µM in chloride conditions, highlighting their synergistic role in chloride-dependent substrate binding.
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The OmcS monomer has <scene name='83/835223/Secondary_structure/2'>remarkably little secondary structure</scene>.
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<center>
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{{Template:ColorKey_Helix}},
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{{Template:ColorKey_310Helix}},
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{{Template:ColorKey_Strand}},
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{{Template:ColorKey_Loop}}.
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</center>
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The structure assigned by the authors is '''77% loops'''; Jmol objectively assigns '''82%''' loops. The authors assigned 10% alpha helices, 7% 3<sub>10</sub> helices, and 6% beta strands.
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The OmcS structure determined by Filman ''et al.'' <ref name="strauss" />was very similar, with '''80%''' loops assigned by the authors (86% by Jmol), having only 3% beta strand but otherwise very similar. We compared OmcS with three other c-type multi-heme cytochrome crystal structures: [[1ofw]], [[3ucp]], and [[3ov0]] had 45%, 49%, and 60% loops respectively.
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===Mechanism of OAT1 inhibition by probenecid===
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The cryo-EM structure of hOAT1 bound to the classic inhibitor probenecid reveals a dual-mechanism of action that goes beyond simple competition, effectively arresting the transporter in a restricted state.
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'''1. Binding Mode and Direct Competition'''
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*Probenecid binds at the top of the central cavity, parallel to the membrane plane.
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*Its binding site overlaps with both Site 1 (partially) and Site 3.
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*It engages in specific, high-affinity interactions with key residues:
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:*K382 on TM8 forms a hydrogen bond with the carboxylate group of probenecid.
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:*Y354 on TM7 forms a hydrogen bond with its sulfonyl group.
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:*Crucially, K382 is also the residue that interacts with the counter-substrate α-ketoglutarate (α-KG), establishing a direct competitive inhibition mechanism by blocking α-KG binding.
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'''2. Conformational Arrest and Cytoplasmic Path Blockage'''
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The primary inhibitory mechanism is a probenecid-induced conformational change that physically blocks substrate access and exit.
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*'''Constriction of the Binding Pocket:''' Compared to the apo state, the cytoplasmic opening of the binding pocket narrows from ~15 Å to ~12 Å in the probenecid-bound state.
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*'''Dual-Pathway Blockade:''' The cytosolic entrance is split into two paths. Probenecid binding critically affects both:
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:*'''Path A''' (between TM2 and TM11) is narrowed from ~5 Å to ~4 Å.
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:*'''Path B''' (between TM5 and TM8) is completely blocked.
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This structural rearrangement is caused by a slight inward movement of the cytoplasmic ends of TM5, TM8, TM10, and TM11 toward the binding pocket.
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'''3. Locked Conformation'''
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By constricting the cytoplasmic access routes, probenecid does not just compete for the substrate-binding site; it stabilizes the transporter in an apo-like, inward-facing conformation that is inaccessible to cytosolic substrates. This prevents the entry of new substrates and likely traps the transporter in this non-functional state, effectively "locking" it and preventing the conformational changes necessary for the transport cycle.
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Each OmcS monomer <scene name='83/835223/Hemes/10'>contains 6 hemes</scene>:
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{{Template:ColorKey_Element_C}}
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{{Template:ColorKey_Element_O}}
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{{Template:ColorKey_Element_N}}
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{{Template:ColorKey_Element_Fe}}.
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The hemes are arranged in [https://en.wikipedia.org/wiki/Stacking_(chemistry) parallel-displaced] pairs. Each pair is orthogonal to the next pair.
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The <scene name='83/835223/Hemes/11'>hemes at each monomer-monomer interface form a parallel-displaced pair</scene>, which likely contributes to the stability of the filament. More importantly, this produces a <scene name='83/835223/Filament/5'>continuous chain of hemes through the length of the filament</scene>. This continuous chain of hemes is believed to be the basis of the electrical conductivity.
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====Full Mechanism of Binding and Inhibition in hOAT1====
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'''Overall Transport Cycle & Substrate Binding (e.g., Olmesartan)'''
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'''1. Outward-Facing State (Hypothesized):''' The transport cycle begins with the transporter in an outward-facing conformation, open to the extracellular space. Substrates and inhibitors from the blood enter the central binding pocket at this stage.
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'''2. Transition to Inward-Facing State:''' Upon binding a substrate like olmesartan, the transporter undergoes a conformational change to the inward-facing state, which is the conformation captured in this study.
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'''3. Substrate Binding and Chloride Coordination in the Inward-Open State:'''
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*Olmesartan docks into Site 3, the polyspecific substrate-binding site, engaging a cage of hydrophobic and aromatic residues (e.g., F438, Y354).
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*Its binding induces specific structural rearrangements, most notably a vertical rotation of the Y230 side chain.
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*Crucially, olmesartan binding creates a favorable environment for chloride ion coordination. The chloride ion is stabilized by a network involving S203, the rotated Y230, and R466.
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*This chloride coordination, facilitated by the species-specific residue S203, is essential for high-affinity binding and efficient translocation of olmesartan. The bottom-gate residues M207 and F442 also interact with the drug, potentially playing a role in its final release into the cytoplasm.
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'''4. Substrate Release:''' The inward-facing conformation with its open paths (Path A and Path B) allows the substrate to dissociate into the cytoplasm. The transporter then likely resets to the outward-facing state, driven by the exchange with intracellular α-ketoglutarate (α-KG).
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'''Inhibition Mechanism (e.g., Probenecid)'''
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The inhibitor probenecid exploits the transport cycle but arrests it through a dual mechanism:
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'''1. Binding and Competition:'''
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*Probenecid enters the binding pocket from the extracellular side and binds in the inward-facing conformation.
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*It occupies Site 3 and partially extends into Site 1. In Site 1, it directly competes with the counter-substrate α-KG by forming a key hydrogen bond with K382, a residue critical for α-KG binding.
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'''2. Conformational Arrest and Cytoplasmic Blockade:'''
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*This is the primary inhibitory mechanism. Probenecid binding induces subtle but critical conformational changes in the cytoplasmic regions of TM5, TM8, TM10, and TM11.
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*These helices shift inward, causing a constriction of the entire cytoplasmic opening of the binding pocket.
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*This constriction completely blocks Path B and severely narrows Path A.
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*By physically obstructing these cytosolic paths, probenecid achieves two things:
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:*It prevents intracellular substrates from entering the binding pocket.
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:*It traps the transporter in a locked, inward-facing, apo-like conformation, preventing the conformational changes needed to complete the transport cycle.
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Each heme is <scene name='83/835223/Heme_cysteine/4'>covalently anchored to two cysteines</scene>, which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls):
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{{Template:ColorKey_Element_C}}
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{{Template:ColorKey_Element_O}}
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{{Template:ColorKey_Element_N}}
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{{Template:ColorKey_Element_S}}
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{{Template:ColorKey_Element_Fe}}.
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12 '''CxxCH''' motifs in the [https://www.uniprot.org/uniprot/Q74A86#sequences OmcS sequence] anchor the 6 hemes within each OmcS chain.
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==Notes & References==
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<references />
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Current revision

Contents

Cryo-EM Structure of the Human TRPV1 Ion Channel

Cryo-EM structure of the human TRPV1 ion channel in the apo state (Liao et al., 2013; ~3.5 Å resolution)

Drag the structure with the mouse to rotate

Introduction

The transient receptor potential vanilloid 1 (TRPV1) ion channel is a heat- and ligand-gated cation channel essential for nociception, inflammatory pain, and thermal sensitivity. Activated by capsaicin, protons, noxious heat (>42°C), and lipid mediators, TRPV1 serves as a polymodal molecular sensor in the peripheral nervous system. Because of its central role in pain signaling, TRPV1 has been a major therapeutic target for developing next-generation analgesics. Understanding its three-dimensional structure is therefore crucial for elucidating its gating mechanism and ligand recognition.

Structural Highlights

Using single-particle cryo-electron microscopy, Liao, Cao, Julius, and Cheng (2013) determined the first near-atomic structures of TRPV1 in multiple functional states, including the apo (resting), capsaicin-bound, and toxin-bound conformations. TRPV1 assembles as a homotetramer, with each subunit containing six transmembrane helices (S1–S6), a re-entrant pore loop, and extensive cytosolic ankyrin repeat domains.

The vanilloid-binding pocket—formed between the S3–S4 helices and the S4–S5 linker—was resolved in detail, explaining how capsaicin stabilizes the open conformation by pulling on the S4–S5 linker and reshaping the S6 helices to widen the pore. Structures bound to the double-knot toxin (DkTx) reveal an even more dilated pore, representing a fully activated gating state. Comparisons across these states demonstrate the sequence of conformational rearrangements that underlie heat and ligand gating in TRPV1.

Significance

These cryo-EM structures provide a mechanistic blueprint for understanding how TRPV1 integrates thermal, chemical, and lipid-derived signals to regulate ion permeation. They reveal conserved gating transitions and define pharmacologically relevant ligand-binding pockets essential for rational drug design. The ability to visualize TRPV1 in distinct activation states enables development of selective analgesic modulators targeting neuropathic and inflammatory pain while minimizing adverse thermo-sensory effects.

References

  • Liao M., Cao E., Julius D., Cheng Y. (2013). Structure of the TRPV1 ion channel determined by electron cryo-microscopy. *Nature*, 504, 107–112.
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