8A4C

Structure of human Rep15:Rab3B complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Rep15 interacts with several Rab GTPases and has a distinct fold for a Rab effector.

Rai, A.Singh, A.K.Bleimling, N.Posern, G.Vetter, I.R.Goody, R.S.

(2022) Nat Commun 13: 4262-4262

  • DOI: https://doi.org/10.1038/s41467-022-31831-1
  • Primary Citation of Related Structures:  
    8A4A, 8A4B, 8A4C

  • PubMed Abstract: 

    In their GTP-bound (active) form, Rab proteins interact with effector proteins that control downstream signaling. One such Rab15 effector is Rep15, which is known to have a role in receptor recycling from the endocytic recycling compartment but otherwise remains poorly characterized. Here, we report the characterization of the Rep15:Rab15 interaction and identification of Rab3 paralogs and Rab34 as Rep15 interacting partners from a yeast two-hybrid assay. Biochemical validation of the interactions is presented and crystal structures of the Rep15:Rab3B and Rep15:Rab3C complexes provide additional mechanistic insight. We find that Rep15 adopts a globular structure that is distinct from other reported Rab15, Rab3 and Rab34 effectors. Structure-based mutagenesis experiments explain the Rep15:Rab interaction specificity. Rep15 depletion in U138MG glioblastoma cells impairs cell proliferation, cell migration and receptor recycling, underscoring the need for further clarification of the role of Rep15 in cancer.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany. amrita.rai@mpi-dortmund.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rab15 effector protein
A, C
238Homo sapiensMutation(s): 1 
Gene Names: REP15
UniProt & NIH Common Fund Data Resources
Find proteins for Q6BDI9 (Homo sapiens)
Explore Q6BDI9 
Go to UniProtKB:  Q6BDI9
GTEx:  ENSG00000174236 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6BDI9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-3B
B, D
221Homo sapiensMutation(s): 0 
Gene Names: RAB3B
UniProt & NIH Common Fund Data Resources
Find proteins for P20337 (Homo sapiens)
Explore P20337 
Go to UniProtKB:  P20337
PHAROS:  P20337
GTEx:  ENSG00000169213 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20337
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.81α = 90
b = 59.22β = 111.9
c = 109.02γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)Germanygrant GO 284/10-1

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description