Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 12.15 kDa 
• Atom Count: 971 
• Residue Count: 102 
• Unique protein chains: 1

3EAZ

Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), C122S mutant.

• DOI: 10.2210/pdb3EAZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-08-26 Released: 2009-11-10 
• Deposition Author(s): Liu, D., Seidel, R.D., Cowburn, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase.

Liu, D., Cowburn, D.

(2016) Biophys Rep 2: 33-43

• PubMed: 27819029 
• DOI: 10.1007/s41048-016-0025-4
• Primary Citation of Related Structures:  
  3EAC, 3EAZ


• PubMed Abstract: 
  

The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.

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Organizational Affiliation: 

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase CSK	A	106	Homo sapiens	Mutation(s): 1  Gene Names: CSK EC: 2.7.10.2
Find proteins for P41240 (Homo sapiens) Explore P41240  Go to UniProtKB:  P41240
NIH Common Fund Data Resources
PHAROS:  P41240 GTEx:  ENSG00000103653

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.226 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.506	α = 90
b = 48.148	β = 90
c = 49.928	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-08-26 
• Released Date: 2009-11-10 
Deposition Author(s): Liu, D., Seidel, R.D., Cowburn, D.

Revision History 

• Version 1.0: 2009-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-07-20
  Changes: Database references
• Version 1.3: 2016-12-14
  Changes: Database references