6wti: Difference between revisions

Latest revision as of 13:56, 13 August 2026

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

Structural highlights

6wti is a 4 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.38Å
Ligands:	3PE, CU, HEM, HEO, U9V, UQ8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CYOB_ECOLI Cytochrome bo(3) ubiquinol terminal oxidase is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at high aeration. Has proton pump activity across the membrane in addition to electron transfer, pumping 2 protons/electron. Protons are probably pumped via D- and K- channels found in this subunit (PubMed:11017202).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.

A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.,Su CC, Lyu M, Morgan CE, Bolla JR, Robinson CV, Yu EW Nat Methods. 2021 Jan;18(1):69-75. doi: 10.1038/s41592-020-01021-2. Epub 2021 Jan, 6. PMID:33408407^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Matsushita K, Patel L, Gennis RB, Kaback HR. Reconstitution of active transport in proteoliposomes containing cytochrome o oxidase and lac carrier protein purified from Escherichia coli. Proc Natl Acad Sci U S A. 1983 Aug;80(16):4889-93. PMID:6308657
↑ Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ. Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol. 2009 Sep;191(17):5510-7. doi: 10.1128/JB.00562-09. Epub 2009 Jun 19. PMID:19542282 doi:https://dx.doi.org/10.1128/JB.00562-09
↑ Sharma P, Hellingwerf KJ, de Mattos MJ, Bekker M. Uncoupling of substrate-level phosphorylation in Escherichia coli during glucose-limited growth. Appl Environ Microbiol. 2012 Oct;78(19):6908-13. doi: 10.1128/AEM.01507-12. Epub , 2012 Jul 27. PMID:22843529 doi:https://dx.doi.org/10.1128/AEM.01507-12
↑ Su CC, Lyu M, Morgan CE, Bolla JR, Robinson CV, Yu EW. A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Nat Methods. 2021 Jan;18(1):69-75. PMID:33408407 doi:10.1038/s41592-020-01021-2

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Matsushita K, Patel L, Gennis RB, Kaback HR. Reconstitution of active transport in proteoliposomes containing cytochrome o oxidase and lac carrier protein purified from Escherichia coli. Proc Natl Acad Sci U S A. 1983 Aug;80(16):4889-93. PMID:6308657

[2] Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ. Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol. 2009 Sep;191(17):5510-7. doi: 10.1128/JB.00562-09. Epub 2009 Jun 19. PMID:19542282 doi:https://dx.doi.org/10.1128/JB.00562-09

[3] Sharma P, Hellingwerf KJ, de Mattos MJ, Bekker M. Uncoupling of substrate-level phosphorylation in Escherichia coli during glucose-limited growth. Appl Environ Microbiol. 2012 Oct;78(19):6908-13. doi: 10.1128/AEM.01507-12. Epub , 2012 Jul 27. PMID:22843529 doi:https://dx.doi.org/10.1128/AEM.01507-12

[4] Su CC, Lyu M, Morgan CE, Bolla JR, Robinson CV, Yu EW. A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Nat Methods. 2021 Jan;18(1):69-75. PMID:33408407 doi:10.1038/s41592-020-01021-2

[1]

[2]

[3]

[4]

@@ Line 5: / Line 5: @@
 <table><tr><td colspan='2'>[[6wti]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WTI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WTI FirstGlance]. <br>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.38&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HEO:HEME+O'>HEO</scene>, <scene name='pdbligand=U9V:pentadecyl(tetradecyl)peroxyanhydride'>U9V</scene>, <scene name='pdbligand=UQ8:UBIQUINONE-8'>UQ8</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PE:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>3PE</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HEO:HEME+O'>HEO</scene>, <scene name='pdbligand=U9V:2-(pentadecanoyloxy)ethyl+hexadecanoate'>U9V</scene>, <scene name='pdbligand=UQ8:UBIQUINONE-8'>UQ8</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6wti FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wti OCA], [https://pdbe.org/6wti PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wti RCSB], [https://www.ebi.ac.uk/pdbsum/6wti PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wti ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/CYOD_ECOLI CYOD_ECOLI] Cytochrome bo(3) ubiquinol terminal oxidase is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at high aeration. Has proton pump activity across the membrane in addition to electron transfer, pumping 2 protons/electron.<ref>PMID:19542282</ref> <ref>PMID:22843529</ref> <ref>PMID:6308657</ref>
+[https://www.uniprot.org/uniprot/CYOB_ECOLI CYOB_ECOLI] Cytochrome bo(3) ubiquinol terminal oxidase is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at high aeration. Has proton pump activity across the membrane in addition to electron transfer, pumping 2 protons/electron. Protons are probably pumped via D- and K- channels found in this subunit (PubMed:11017202).<ref>PMID:6308657</ref> <ref>PMID:19542282</ref> <ref>PMID:22843529</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (&lt;100 kDa) and less abundant (&lt;10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
+A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.,Su CC, Lyu M, Morgan CE, Bolla JR, Robinson CV, Yu EW Nat Methods. 2021 Jan;18(1):69-75. doi: 10.1038/s41592-020-01021-2. Epub 2021 Jan, 6. PMID:33408407<ref>PMID:33408407</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6wti" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

6wti: Difference between revisions

Latest revision as of 13:56, 13 August 2026

The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools