2HT6

Crystal structure of Human Gem G-domain bound to GDP

• PDB DOI: https://doi.org/10.2210/pdb2HT6/pdb

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


• Deposited: 2006-07-25 Released: 2006-10-31 
• Deposition Author(s): Opatowsky, Y., Hirsch, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structure-function studies of the G-domain from human gem, a novel small G-protein.

Opatowsky, Y., Sasson, Y., Shaked, I., Ward, Y., Chomsky-Hecht, O., Litvak, Y., Selinger, Z., Kelly, K., Hirsch, J.A.

(2006) FEBS Lett 580: 5959-5964

• PubMed: 17052716 
• DOI: https://doi.org/10.1016/j.febslet.2006.09.067
• Primary Citation of Related Structures:  
  2HT6


• PubMed Abstract: 
  

  Gem, a member of the Rad,Gem/Kir subfamily of small G-proteins, has unique sequence features. We report here the crystallographic structure determination of the Gem G-domain in complex with nucleotide to 2.4 A resolution. Although the basic Ras protein fold is maintained, the Gem switch regions emphatically differ from the Ras paradigm. Our ensuing biochemical characterization indicates that Gem G-domain markedly prefers GDP over GTP. Two known functions of Gem are distinctly affected by spatially separated clusters of mutations.

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Organizational Affiliation: 

Department of Biochemistry, Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv 69978, Israel.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.16 kDa 
• Atom Count: 2,765 
• Modelled Residue Count: 331 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein GEM	A, B	174	Homo sapiens	Mutation(s): 0  Gene Names: GEM, KIR
UniProt & NIH Common Fund Data Resources
Find proteins for P55040 (Homo sapiens) Explore P55040  Go to UniProtKB:  P55040
PHAROS:  P55040 GTEx:  ENSG00000164949

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.843	α = 90
b = 81.433	β = 90
c = 124.095	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-31 
Deposition Author(s): Opatowsky, Y., Hirsch, J.A.

Revision History  

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description