Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 20.09 kDa 
• Atom Count: 1734 
• Modelled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1

1R2Q

Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution

• PDB DOI: 10.2210/pdb1R2Q/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-09-29 Released: 2003-12-23 
• Deposition Author(s): Terzyan, S., Zhu, G., Li, G., Zhang, X.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.169 
• R-Value Work: 0.124 
• R-Value Observed: 0.124 

Literature

Refinement of the structure of human Rab5a GTPase domain at 1.05 A resolution.

Terzyan, S., Zhu, G., Li, G., Zhang, X.C.

(2004) Acta Crystallogr D Biol Crystallogr 60: 54-60

• PubMed: 14684892 
• DOI: 10.1107/s0907444903021632
• Primary Citation of Related Structures:  
  1R2Q


• PubMed Abstract: 
  

Rab5 is a GTPase that regulates early endosome fusion. Its GTPase domain crystal structure is reported here at 1.05 A resolution in complex with a GTP-analog molecule. It provides the highest resolution three-dimensional model so far obtained for proteins from the Ras-like GTPase family. This study allows extension of structural examination of the GTPase machinery as well as of high-resolution protein structures in general. For example, a buried water-molecule network was observed underneath the switch regions, which is consistent with the functional roles of these regions in the molecular-switching process. Furthermore, residues of multiple conformation and clustered distribution of anisotropic thermal motions of the protein molecule may have general implications for the function of Ras-like GTPases.

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Organizational Affiliation: 

Crystallography Research Program of Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-5A	A	170	Homo sapiens	Mutation(s): 0  Gene Names: RAB5A OR RAB5, RAB5A, RAB5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P20339 (Homo sapiens) Explore P20339  Go to UniProtKB:  P20339
PHAROS:  P20339 GTEx:  ENSG00000144566

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
GOL	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.169 
• R-Value Work: 0.124 
• R-Value Observed: 0.124 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.727	α = 90
b = 64.573	β = 90
c = 66.18	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
SHELXL-97	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-29 
• Released Date: 2003-12-23 
Deposition Author(s): Terzyan, S., Zhu, G., Li, G., Zhang, X.C.

Revision History  

• Version 1.0: 2003-12-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance