Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58251.09 
• Atom Count: 3074 
• Residue Count: 494 
• Unique protein chains: 2

4N3Z

Crystal structure of Rabex-5delta and Rabaptin-5C21 complex

• DOI: 10.2210/pdb4N3Z/pdb

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


• Deposited: 2013-10-08 Released: 2014-07-23 
• Deposition Author(s): Zhang, Z., Zhang, T., Ding, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.315 
• R-Value Work: 0.264 

Literature

Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5

Zhang, Z., Zhang, T., Wang, S., Gong, Z., Tang, C., Chen, J., Ding, J.

(2014) Elife 3: e02687-e02687

• PubMed: 24957337 
• DOI: 10.7554/eLife.02687
• Primary Citation of Related Structures:  
  4Q9U, 4N3Y, 4N3X


• PubMed Abstract: 
  

Rabex-5 and Rabaptin-5 function together to activate Rab5 and further promote early endosomal fusion in endocytosis. The Rabex-5 GEF activity is autoinhibited by the Rabex-5 CC domain (Rabex-5CC) and activated by the Rabaptin-5 C2-1 domain (Rabaptin-5C21) with yet unknown mechanism. We report here the crystal structures of Rabex-5 in complex with the dimeric Rabaptin-5C21 (Rabaptin-5C212) and in complex with Rabaptin-5C212 and Rab5, along with biophysical and biochemical analyses. We show that Rabex-5CC assumes an amphipathic α-helix which binds weakly to the substrate-binding site of the GEF domain, leading to weak autoinhibition of the GEF activity. Binding of Rabaptin-5C21 to Rabex-5 displaces Rabex-5CC to yield a largely exposed substrate-binding site, leading to release of the GEF activity. In the ternary complex the substrate-binding site of Rabex-5 is completely exposed to bind and activate Rab5. Our results reveal the molecular mechanism for the regulation of the Rabex-5 GEF activity.

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Organizational Affiliation: 

State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Rab5 GDP/GTP exchange factor	A	310	Homo sapiens	Mutation(s): 0  Gene Names: RABGEF1 (RABEX5)
Find proteins for Q9UJ41 (Homo sapiens) Go to Gene View: RABGEF1 Go to UniProtKB:  Q9UJ41

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Rab GTPase-binding effector protein 1	B, C	92	Homo sapiens	Mutation(s): 0  Gene Names: RABEP1 (RAB5EP, RABPT5, RABPT5A)
Find proteins for Q15276 (Homo sapiens) Go to Gene View: RABEP1 Go to UniProtKB:  Q15276

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A, B, C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.315 
• R-Value Work: 0.264 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 87.140	α = 90.00
b = 87.140	β = 90.00
c = 168.878	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
HKL-2000	data collection
PDB_EXTRACT	data extraction
PHASER	phasing
SCALEPACK	data scaling
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-10-08 
• Released Date: 2014-07-23 
• Deposition Author(s): Zhang, Z., Zhang, T., Ding, J.

Revision History 

• Version 1.0: 2014-07-23
  Type: Initial release
• Version 1.1: 2015-12-09
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Refinement description