4LHV | pdb_00004lhv

Crystal structure of Rab8 in its inactive GDP-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.244 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4LHV

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

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 Biological Chem 288: 32466-32474

  • DOI: https://doi.org/10.1074/jbc.M113.498329
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 102.18 kDa 
  • Atom Count: 6,901 
  • Modeled Residue Count: 792 
  • Deposited Residue Count: 870 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
EC: 3.6.5.2
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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.244 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
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
PHASESphasing
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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