9Z7E | pdb_00009z7e

Crystal structure of Vps29 in complex with C. thermophilum Gyp6L (87 to 107)

PDB DOI: https://doi.org/10.2210/pdb9Z7E/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Mus musculus, Thermochaetoides thermophila
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-11-17 Released: 2026-10-28
Deposition Author(s): Chen, K.-E., Collins, B.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.265 (Depositor), 0.263 (DCC)
R-Value Work:
0.203 (Depositor), 0.203 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Z7E

This is version 1.0 of the entry. See complete history.

Literature

The GTPase activating protein Gyp6 binds Retromer and inactivates Rab7/Ypt7 to coordinate the formation of endosomal carriers

Alves, A.C., Chen, K.E., Mayer, L.M., Guo, Q., Stephens, E.J., Liu, M., Healy, M.D., Collins, B.M., Mayer, A.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.01.23.701266

Macromolecule Content

Total Structure Weight: 23.34 kDa
Atom Count: 1,545
Modeled Residue Count: 188
Deposited Residue Count: 209
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Vacuolar protein sorting-associated protein 29	A	188	Mus musculus	Mutation(s): 0 Gene Names: Vps29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZ88 (Mus musculus) Explore Q9QZ88 Go to UniProtKB: Q9QZ88
IMPC: MGI:1928344
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9QZ88
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase-activating protein GYP6 like protein	B	21	Thermochaetoides thermophila	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
SCY Query on SCY	A	CYS	Acetylation	C₅ H₉ N O₃ S

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.265 (Depositor), 0.263 (DCC)
R-Value Work: 0.203 (Depositor), 0.203 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.399	α = 90
b = 72.125	β = 90
c = 114.358	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP2016410

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release