1SEM | pdb_00001sem

STRUCTURAL DETERMINANTS OF PEPTIDE-BINDING ORIENTATION AND OF SEQUENCE SPECIFICITY IN SH3 DOMAINS

• PDB DOI: https://doi.org/10.2210/pdb1SEM/pdb

• Classification: SIGNAL TRANSDUCTION PROTEIN
• Organism(s): Caenorhabditis elegans, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1995-03-28 Released: 1995-07-10 
• Deposition Author(s): Lim, W.A., Richards, F.M., Fox, R.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.189 (Depositor) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains.

Lim, W.A., Richards, F.M., Fox, R.O.

(1994) Nature 372: 375-379

• PubMed: 7802869 
• DOI: https://doi.org/10.1038/372375a0
• Primary Citation Related Structures: 
  1SEM


• PubMed Abstract: 
  

  The Src-homology-3 (SH3) domains of the Caenorhabditis elegans protein SEM-5 and its human and Drosophila homologues, Grb2 and Drk (refs 1-4), bind proline-rich sequences found in the nucleotide-exchange factor Sos as part of their proposed function linking receptor tyrosine kinase activation to Ras activation. Here we report the crystal structure at 2.0 A resolution of the carboxy-terminal SH3 domain from SEM-5 complexed to the mSos-derived amino-acid sequence PPPVPPRRR. The peptide is found to bind in an orientation ('minus') that is precisely opposite to that observed previously ('plus' orientation) in other SH3-peptide complexes. This novel ability of peptide-recognition proteins to recognize peptides in two distinct modes may play an important role in the signalling specificity of pathways involving SH3 domains. Comparison of this structure with other SH3 complexes reveals how a conserved binding face can be used to recognize peptides in different orientations, and why the Sos peptide binds in this particular orientation.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 15.8 kDa 
• Atom Count: 1,128 
• Modeled Residue Count: 131 
• Deposited Residue Count: 136 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEM-5	A, B	58	Caenorhabditis elegans	Mutation(s): 0  Gene Names: GRB2
UniProt
Find proteins for P29355 (Caenorhabditis elegans) Explore P29355  Go to UniProtKB:  P29355

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
10-RESIDUE PROLINE-RICH PEPTIDE FROM MSOS (ACE-PRO-PRO-PRO-VAL-PRO-PRO-ARG-ARG-ARG)	C, D	10	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.189 (Depositor) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.912	α = 90
b = 68.41	β = 94.71
c = 35.029	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-07-10 
Deposition Author(s): Lim, W.A., Richards, F.M., Fox, R.O.

Revision History  

• Version 1.0: 1995-07-10
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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, Structure summary