8RKS | pdb_00008rks

Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.288 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.251 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.256 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Retromer-mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21.

Romano-Moreno, M.Astorga-Simon, E.N.Rojas, A.L.Hierro, A.

(2024) Protein Sci 33: e4980-e4980

  • DOI: https://doi.org/10.1002/pro.4980
  • Primary Citation of Related Structures:  
    8RKS

  • PubMed Abstract: 

    Endosomal trafficking ensures the proper distribution of lipids and proteins to various cellular compartments, facilitating intracellular communication, nutrient transport, waste disposal, and the maintenance of cell structure. Retromer, a peripheral membrane protein complex, plays an important role in this process by recruiting the associated actin-polymerizing WASH complex to establish distinct sorting domains. The WASH complex is recruited through the interaction of the VPS35 subunit of retromer with the WASH complex subunit FAM21. Here, we report the identification of two separate fragments of FAM21 that interact with VPS35, along with a third fragment that binds to the VPS29 subunit of retromer. The crystal structure of VPS29 bound to a peptide derived from FAM21 shows a distinctive sharp bend that inserts into a conserved hydrophobic pocket with a binding mode similar to that adopted by other VPS29 effectors. Interestingly, despite the network of interactions between FAM21 and retromer occurring near the Parkinson's disease-linked mutation (D620N) in VPS35, this mutation does not significantly impair the direct association with FAM21 in vitro.


  • Organizational Affiliation
    • Center for Cooperative Research in Biosciences (CIC bioGUNE), Bilbao, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29
A, C, E, G
182Homo sapiensMutation(s): 0 
Gene Names: VPS29DC15DC7MDS007
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ0 (Homo sapiens)
Explore Q9UBQ0 
Go to UniProtKB:  Q9UBQ0
PHAROS:  Q9UBQ0
GTEx:  ENSG00000111237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBQ0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 35
B, D, F, H
311Homo sapiensMutation(s): 0 
Gene Names: VPS35MEM3TCCCTA00141
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QK1 (Homo sapiens)
Explore Q96QK1 
Go to UniProtKB:  Q96QK1
PHAROS:  Q96QK1
GTEx:  ENSG00000069329 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QK1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
WASH complex subunit 2AI [auth K],
J [auth I],
K [auth J],
L
7Homo sapiensMutation(s): 0 
Gene Names: WASHC2AFAM21AFAM21B
UniProt & NIH Common Fund Data Resources
Find proteins for Q641Q2 (Homo sapiens)
Explore Q641Q2 
Go to UniProtKB:  Q641Q2
GTEx:  ENSG00000099290 
Entity Groups  
UniProt GroupQ641Q2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.288 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.251 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.256 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.267α = 90
b = 139.095β = 90
c = 146.147γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2020-119132GB-I00
Ministry of Economy and Competitiveness (MINECO)SpainBFU2017-88766-R

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release