2J06 | pdb_00002j06

Crystal structure of the RasGAP SH3 domain at 1.8 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb2J06/pdb

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


• Deposited: 2006-08-01 Released: 2007-01-02 
• Deposition Author(s): Ross, B., Gajhede, M., Kristensen, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

High Resolution Crystal Structures of the P120 Rasgap SH3 Domain.

Ross, B., Kristensen, O., Favre, D., Walicki, J., Kastrup, J.S., Widmann, C., Gajhede, M.

(2007) Biochem Biophys Res Commun 353: 463

• PubMed: 17188236 
• DOI: https://doi.org/10.1016/j.bbrc.2006.12.044
• Primary Citation Related Structures: 
  2J05, 2J06


• PubMed Abstract: 
  

  X-ray structures of two crystal forms of the Src homology 3 domain (SH3) of the Ras GTPase activating protein (RasGAP) were determined at 1.5 and 1.8A resolution. The overall structure comprises a single domain with two tightly packed beta-sheets linked by a short helical segment. An important motif for peptide binding in other SH3 domains is not conserved in RasGAP. The RasGAP SH3 domain forms dimers in the crystal structures, which may provide new functional insight. The dimer interface involves residues also present in a peptide previously identified as an apoptotic sensitizer of tumor cells.

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Organizational Affiliation: 
• Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 15.53 kDa 
• Atom Count: 1,094 
• Modeled Residue Count: 122 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS GTPASE-ACTIVATING PROTEIN 1	A, B	65	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20936 (Homo sapiens) Explore P20936  Go to UniProtKB:  P20936
PHAROS:  P20936 GTEx:  ENSG00000145715

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.240 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.61	α = 90
b = 33.61	β = 90
c = 196.33	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Ross, B., Gajhede, M., Kristensen, O.

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary