4LHZ

Crystal structure of GTP-bound Rab8:Rabin8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 

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Ligand Structure Quality Assessment 


This is version 1.1 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 Biol Chem 288: 32466-32474

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

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-8AA, B186Homo 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rab-3A-interacting proteinC, D, E, F78Homo sapiensMutation(s): 0 
Gene Names: RAB3IPRABIN8
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QF0 (Homo sapiens)
Explore Q96QF0 
Go to UniProtKB:  Q96QF0
PHAROS:  Q96QF0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A], H [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.278 
  • R-Value Observed: 0.279 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.337α = 90
b = 165.561β = 90
c = 167.263γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASESphasing
REFMACrefinement
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