8KB8 | pdb_00008kb8

Structure of the WDR91 WD40 domain complexed with Rab7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Insights into the distinct membrane targeting mechanisms of WDR91 family proteins.

Ma, X.Li, J.Liu, N.Banerjee, S.Hu, X.Wang, X.Dong, J.Liu, K.Yang, C.Dong, Z.

(2024) Structure 32: 2287-2300.e4

  • DOI: https://doi.org/10.1016/j.str.2024.09.023
  • Primary Citation Related Structures: 
    8KB8, 8KB9

  • PubMed Abstract: 

    WDR91 and SORF1, members of the WD repeat-containing protein 91 family, control phosphoinositide conversion by inhibiting phosphatidylinositol 3-kinase activity on endosomes, which promotes endosome maturation. Here, we report the crystal structure of the human WDR91 WD40 domain complexed with Rab7 that has an unusual interface at the C-terminus of the Rab7 switch II region. WDR91 is highly selective for Rab7 among the tested GTPases. A LIS1 homology (LisH) motif within the WDR91 N-terminal domain (NTD) mediates self-association and may contribute partly to the augmented interaction between full-length WDR91 and Rab7. Both the Rab7 binding site and the LisH motif are indispensable for WDR91 function in endocytic trafficking. For the WDR91 orthologue SORF1 lacking the C-terminal WD40 domain, a C-terminal amphipathic helix (AH) mediates strong interactions with liposomes containing acidic lipids. During evolution the human WDR91 ancestor gene might have acquired a WD40 domain to replace the AH for endosomal membrane targeting.


  • Organizational Affiliation
    • China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan 450003, China.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 91
A, B
363Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4D1P6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7a
C, D
181Homo sapiensMutation(s): 1 
Gene Names: RAB7A
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
PHAROS:  P51149
GTEx:  ENSG00000075785 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51149
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.261 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.452α = 90
b = 81.077β = 94.406
c = 116.404γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-07
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-18
    Changes: Database references