8A4C | pdb_00008a4c

Structure of human Rep15:Rab3B complex.

• PDB DOI: https://doi.org/10.2210/pdb8A4C/pdb

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


• Deposited: 2022-06-10 Released: 2022-08-10 
• Deposition Author(s): Rai, A., Vetter, I.R., Goody, R.S.
• Funding Organization(s): Max Planck Society, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

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

• PubMed: 35871249 
• 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.

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Organizational Affiliation: 
• Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany. [e-mail].
Institute for Physiological Chemistry, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 104.65 kDa 
• Atom Count: 6,209 
• Modeled Residue Count: 744 
• Deposited Residue Count: 918 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab15 effector protein	A, C	238	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-3B	B, D	221	Homo sapiens	Mutation(s): 0  Gene Names: RAB3B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P20337 (Homo sapiens) Explore P20337  Go to UniProtKB:  P20337
PHAROS:  P20337 GTEx:  ENSG00000169213

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	E [auth B], G [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	F [auth B], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.81	α = 90
b = 59.22	β = 111.9
c = 109.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Rai, A., Vetter, I.R., Goody, R.S.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--
German Research Foundation (DFG)	Germany	grant GO 284/10-1

Revision History  

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