3E5H | pdb_00003e5h

Crystal Structure of Rab28 GTPase in the Active (GppNHp-bound) Form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.181 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.151 (Depositor) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Large nucleotide-dependent conformational change in Rab28.

Lee, S.H., Baek, K., Dominguez, R.

(2008) FEBS Lett 582: 4107-4111

  • DOI: https://doi.org/10.1016/j.febslet.2008.11.008
  • Primary Citation Related Structures: 
    3E5H

  • PubMed Abstract: 

    Rab GTPases are essential regulators of membrane trafficking. We report crystal structures of Rab28 in the active (GppNHp-bound) and inactive (GDP-3'P-bound) forms at 1.5 and 1.1A resolution. Rab28 is a distant member of the Rab family. While the overall fold of Rab28 resembles that of other Rab GTPases, it undergoes a larger nucleotide-dependent conformational change than other members of this family. Added flexibility resulting from a double-glycine motif at the beginning of switch 2 might partially account for this observation. The double-glycine motif, which is conserved in the Arf family, only occurs in Rab28 and Rab7B of the Rab family, and may have a profound effect on their catalytic activities.

    • Organizational Affiliation: 
    • Department of Physiology, University of Pennsylvania School of Medicine, 3700 Hamilton Walk, A507 Richards Building, Philadelphia, PA 19104-6085, USA.

Macromolecule Content 

  • Total Structure Weight: 20.71 kDa 
  • Atom Count: 1,771 
  • Modeled Residue Count: 177 
  • Deposited Residue Count: 178 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ras-related protein Rab-28178Homo sapiensMutation(s): 0 
Gene Names: rab28
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51157 (Homo sapiens)
Explore P51157 
Go to UniProtKB:  P51157
PHAROS:  P51157
GTEx:  ENSG00000157869 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51157
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.181 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.151 (Depositor) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.747α = 90
b = 79.747β = 90
c = 66.977γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description