Crystal structure of Rab8 in its inactive GDP-bound form

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.2 of the entry. See complete history


Intermediates in the Guanine Nucleotide Exchange Reaction of Rab8 Protein Catalyzed by Guanine Nucleotide Exchange Factors Rabin8 and GRAB.

Guo, Z.Hou, X.Goody, R.S.Itzen, A.

(2013) J Biol Chem 288: 32466-32474

  • DOI: https://doi.org/10.1074/jbc.M113.498329
  • Primary Citation of Related Structures:  
    4LHV, 4LHW, 4LHX, 4LHY, 4LHZ, 4LI0

  • PubMed Abstract: 

    Small G-proteins of the Ras superfamily control the temporal and spatial coordination of intracellular signaling networks by acting as molecular on/off switches. Guanine nucleotide exchange factors (GEFs) regulate the activation of these G-proteins through catalytic replacement of GDP by GTP. During nucleotide exchange, three distinct substrate·enzyme complexes occur: a ternary complex with GDP at the start of the reaction (G-protein·GEF·GDP), an intermediary nucleotide-free binary complex (G-protein·GEF), and a ternary GTP complex after productive G-protein activation (G-protein·GEF·GTP). Here, we show structural snapshots of the full nucleotide exchange reaction sequence together with the G-protein substrates and products using Rabin8/GRAB (GEF) and Rab8 (G-protein) as a model system. Together with a thorough enzymatic characterization, our data provide a detailed view into the mechanism of Rabin8/GRAB-mediated nucleotide exchange.

  • Organizational Affiliation

    From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-8A
A, B, C, D, E
174Homo sapiensMutation(s): 0 
Gene Names: RAB8AMELRAB8
UniProt & NIH Common Fund Data Resources
Find proteins for P61006 (Homo sapiens)
Explore P61006 
Go to UniProtKB:  P61006
PHAROS:  P61006
GTEx:  ENSG00000167461 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61006
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
C10 H15 N5 O11 P2
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E]
Binding Affinity Annotations 
IDSourceBinding Affinity
GDP PDBBind:  4LHV Kd: 0.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.836α = 90
b = 75.95β = 98.44
c = 106.618γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description