8KB8

Structure of the WDR91 WD40 domain complexed with Rab7

• PDB DOI: https://doi.org/10.2210/pdb8KB8/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-08-04 Released: 2024-08-07 
• Deposition Author(s): Li, J., Ma, X.L., Banerjee, S., Dong, Z.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Starting Models: experimental

Literature

Structure of the WDR91 WD40 domain complexed with Rab7

Li, J., Ma, X.L., Banerjee, S., Dong, Z.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 121.56 kDa 
• Atom Count: 7,985 
• Modelled Residue Count: 1,016 
• Deposited Residue Count: 1,088 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 91	A, B	363	Homo sapiens	Mutation(s): 0  Gene Names: WDR91
UniProt & NIH Common Fund Data Resources
Find proteins for A4D1P6 (Homo sapiens) Explore A4D1P6  Go to UniProtKB:  A4D1P6
PHAROS:  A4D1P6 GTEx:  ENSG00000105875

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-7a	C, D	181	Homo sapiens	Mutation(s): 1  Gene Names: RAB7A
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens) Explore P51149  Go to UniProtKB:  P51149
PHAROS:  P51149 GTEx:  ENSG00000075785

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	F [auth C], H [auth D]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	E [auth C], G [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.452	α = 90
b = 81.077	β = 94.406
c = 116.404	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Li, J., Ma, X.L., Banerjee, S., Dong, Z.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release