9vlb | pdb_00009vlb

Crystal Structure of a GDP-bound Bombyx mori RabX6

spinqualitylabelsall models 9vlb, resolution 3.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9vlb is a 2 chain structure with sequence from Bombyx mori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.1Å Ligands: GDP, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q2F5M5_BOMMO Publication Abstract from PubMed Rab GTPases are molecular switches that control intracellular vesicular transport by cycling between GDP- and GTP-bound states. Insects encode an insect-specific subset, RabX; Bombyx mori RabX6 (BmRabX6) has been implicated in testis development and neuropeptide secretion, but its structure and mechanism were unknown. Here we report the 3.1 A crystal structure of BmRabX6 in complex with GDP and Mg2+ (PDB: 9VLB), the first structure of an insect-specific Rab GTPase. BmRabX6 adopts the canonical small GTPase fold with conserved P-loop and Switch I/II, and displays a GDP-binding mode similar to vertebrate Rabs. Two features distinguish BmRabX6. First, the catalytic glutamine required for GTP hydrolysis in typical Rabs is naturally replaced by methionine (Met69) and oriented away from the nucleotide, consistent with obligate GAP-assisted hydrolysis. Second, one residue of the hydrophobic effector-binding triad is histidine (His47), suggesting a potential shift toward a hydrophilic interface-mediated interaction distinct from canonical Rab-effector recognition. AlphaFold3-based complex modeling further identified BmH9J2P5 as a prioritized GTPase-activating protein (GAP) candidate interacting with BmRabX6. These adaptations suggest that BmRabX6 preserves core nucleotide cycling while employing divergent regulatory chemistry tuned to insect physiology. Our structure provides a framework for testing GAP dependence and effector specificity of RabX6 in reproductive and neuronal tissues and illustrates how strategic amino-acid substitutions diversify Rab function. Crystal Structure of a GDP-bound Bombyx mori RabX6.,Urushihara R, Umemoto Y, Liu J, Nishimoto E, Teramoto T, Kakuta Y, Uno T J Biochem. 2025 Nov 21:mvaf071. doi: 10.1093/jb/mvaf071. PMID:41268670 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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