8FUD | pdb_00008fud

Crystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)

• PDB DOI: https://doi.org/10.2210/pdb8FUD/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Mus musculus, Thermochaetoides thermophila DSM 1495
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-17 Released: 2024-07-24 
• Deposition Author(s): Chen, K.-E., Collins, B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.203 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.177 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer

Chen, K.E., Tillu, V.A., Gopaldass, N., Chowdhury, S.R., Leneva, N., Kovtun, O., Ruan, J., Guo, Q., Ariotti, N., Mayer, A., Collins, B.M.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.03.24.586500

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.5 kDa 
• Atom Count: 3,441 
• Modeled Residue Count: 387 
• Deposited Residue Count: 396 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 29	A, B	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative vacuolar protein sorting-associated protein	C, D	10	Thermochaetoides thermophila DSM 1495	Mutation(s): 0
UniProt
Find proteins for G0SH11 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SH11  Go to UniProtKB:  G0SH11

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.203 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.177 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.051	α = 90
b = 68.597	β = 90
c = 211.139	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Chen, K.-E., Collins, B.

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

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release