Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 15.58 kDa 
• Atom Count: 975 
• Residue Count: 110 
• Unique protein chains: 2

3MAZ

Crystal Structure of the Human BRDG1/STAP-1 SH2 Domain in Complex with the NTAL pTyr136 Peptide

• DOI: 10.2210/pdb3MAZ/pdb

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


• Deposited: 2010-03-24 Released: 2010-05-12 
• Deposition Author(s): Kaneko, T., Huang, H., Zhao, B., Li, L., Liu, H., Voss, C.K., Wu, C., Schiller, M.R., Li, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Loops govern SH2 domain specificity by controlling access to binding pockets.

Kaneko, T., Huang, H., Zhao, B., Li, L., Liu, H., Voss, C.K., Wu, C., Schiller, M.R., Li, S.S.

(2010) Sci Signal 3: ra34-ra34

• PubMed: 20442417 
• DOI: 10.1126/scisignal.2000796
• Primary Citation of Related Structures:  
  3MAZ


• PubMed Abstract: 
  

Cellular functions require specific protein-protein interactions that are often mediated by modular domains that use binding pockets to engage particular sequence motifs in their partners. Yet, how different members of a domain family select for distinct sequence motifs is not fully understood. The human genome encodes 120 Src homology 2 (SH2) domains (in 110 proteins), which mediate protein-protein interactions by binding to proteins with diverse phosphotyrosine (pTyr)-containing sequences. The structure of the SH2 domain of BRDG1 bound to a peptide revealed a binding pocket that was blocked by a loop residue in most other SH2 domains. Analysis of 63 SH2 domain structures suggested that the SH2 domains contain three binding pockets, which exhibit selectivity for the three positions after the pTyr in a peptide, and that SH2 domain loops defined the accessibility and shape of these pockets. Despite sequence variability in the loops, we identified conserved structural features in the loops of SH2 domains responsible for controlling access to these surface pockets. We engineered new loops in an SH2 domain that altered specificity as predicted. Thus, selective blockage of binding subsites or pockets by surface loops provides a molecular basis by which the diverse modes of ligand recognition by the SH2 domain may have evolved and provides a framework for engineering SH2 domains and designing SH2-specific inhibitors.

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Organizational Affiliation: 

Department of Biochemistry and the Siebens-Drake Research Institute, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada N6A 5C1.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal-transducing adaptor protein 1	A	125	Homo sapiens	Mutation(s): 1  Gene Names: STAP1, BRDG1
Find proteins for Q9ULZ2 (Homo sapiens) Explore Q9ULZ2  Go to UniProtKB:  Q9ULZ2
NIH Common Fund Data Resources
PHAROS:  Q9ULZ2 GTEx:  ENSG00000035720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CheD family protein	B	12	N/A	Mutation(s): 2
Find proteins for Q9GZY6 (Homo sapiens) Explore Q9GZY6  Go to UniProtKB:  Q9GZY6
NIH Common Fund Data Resources
PHAROS:  Q9GZY6 GTEx:  ENSG00000086730

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	A	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.236 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.64	α = 90
b = 72.64	β = 90
c = 97.84	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-24 
• Released Date: 2010-05-12 
Deposition Author(s): Kaneko, T., Huang, H., Zhao, B., Li, L., Liu, H., Voss, C.K., Wu, C., Schiller, M.R., Li, S.S.

Revision History 

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance