1HCT

NMR STRUCTURE OF THE HUMAN SRC SH2 DOMAIN COMPLEX


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 23 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the human pp60c-src SH2 domain complexed with a phosphorylated tyrosine pentapeptide.

Xu, R.X.Word, J.M.Davis, D.G.Rink, M.J.Willard Jr., D.H.Gampe Jr., R.T.

(1995) Biochemistry 34: 2107-2121

  • Primary Citation of Related Structures:  1HCS

  • PubMed Abstract: 
  • Human pp60c-src is a cellular nonreceptor tyrosine kinase that participates in cytosolic signal transduction and has been implicated in the development of malignant tumors in the human breast and colon. Signal transduction is mediated by highly speci ...

    Human pp60c-src is a cellular nonreceptor tyrosine kinase that participates in cytosolic signal transduction and has been implicated in the development of malignant tumors in the human breast and colon. Signal transduction is mediated by highly specific interactions between the SH2 domain and receptor phosphorylated tyrosine binding motifs. To elucidate the molecular conformation and interactions in solution, a family of highly resolved nuclear magnetic resonance (NMR) structures was determined for the src SH2 domain complexed with a high-affinity phosphorylated pentapeptide, acetyl-p YEEIE-OH. The 23 structures, generated with a distance geometry (DG) and a dynamical simulated annealing (SA) procedure, satisfied 2072 experimental restraints derived from a variety of multifrequency/multidimensional and isotope-filtered NMR data. Superimposition of residues 143-245 upon the mean coordinate set yielded an atomic rmsd of 0.58 +/- 0.09 A for the N, C alpha, C' atoms and 1.04 +/- 0.08 for all the non-hydrogen atoms. Residues in the ordered secondary structure regions superimpose to 0.29 +/- 0.04 A for the N, C alpha, C' and 0.73 +/- 0.08 A for all the non-hydrogen atoms. The angular order parameter calculated for the phi, psi angles was > 0.9 for 81 of the 106 protein residues. The main protein conformational features are three antiparallel beta-strands that traverse a compact core with an alpha-helix on each side of the core near the N- and C-termini. The observed intermolecular nuclear Overhauser effects (NOE) from the pY, +1E, and +3I residues positioned the ligand in an extended conformation across the SH2 domain surface with the pY and +3I side chains inserted into the protein binding pockets. In general, the protein conformation is consistent with previously reported structures of different SH2 domain complexes determined by X-ray crystallography. However, inter- or intramolecular interactions involving the guanidinium side chains of the solvated R alpha A2 or the buried R beta B5 were not observed at pH = 5.5 or 7.0. If such interactions exist in solution, the absence of any confirming data probably arises from rapid exchange with solvent and/or undetermined dynamic components. Thus, the unrestrained R alpha A2 side chain did not show an amino-aromatic interaction or a hydrogen bond to the -1 carbonyl oxygen as observed in the crystal structures. This result is consistent with the solution structure of a different SH2 domain complex. A more detailed comparison between the crystal structure and the NMR-derived solution structures of the same src SH2 domain complex is presented.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • Nuclear Magnetic Resonance Structure of an Sh2 Domain of Phospholipase C-Gamma1 Complexed with a High Affinity Binding Peptide
      Pascal, S.M.,Singer, A.U.,Gish, G.,Yamazaki, T.,Shoelson, S.E.,Pawson, T.,Kay, L.E.,Forman-Kay, J.D.
      (1994) Cell 77: 461
    • Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms
      Waksman, G.,Shoelson, S.E.,Pant, N.,Cowburn, D.,Kuriyan, J.
      (1993) Cell 72: 779
    • Recognition of a High-Affinity Phosphotyrosyl Peptide by the Src Homology-2 Domain of P56Lck
      Eck, M.J.,Shoelson, S.E.,Harrison, S.C.
      (1993) Nature 362: 87
    • Human Cellular Src Gene: Nucleotide Sequence and Derived Amino Acid Sequence of the Region Coding for the Carboxy-Terminal Two-Thirds of Pp60C-Src
      Anderson, S.K.,Gibbs, C.P.,Tanaka, A.,Kung, H.J.,Fugita, D.J.
      (1985) Mol.Cell.Biol. 5: 1122
    • Peptide Inhibitors of Src SH3-Sh2(Slash)Phosphoprotein Interactions
      Gilmer, T.,Rodriguez, M.,Jordan, S.,Crosby, R.,Alligood, K.,Green, M.,Kimery, M.,Wagner, C.,Kinder, D.,Charifson, P.,Hassell, A.M.,Willard, D.,Luther, M.,Rusnak, D.,Sternbach, D.D.,Mehrotra, M.,Peel, M.,Shampine, L.,Davis, R.,Robbins, J.,Patel, I.R.,Kassel, D.,Burkhart, W.,Moyer, M.,Bradshaw, T.,Berman, J.
      (1994) J.Biol.Chem. 269: 31711


    Organizational Affiliation

    Molecular Sciences Division, Glaxo Research Institute, Research Triangle Park, North Carolina 27709.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYL-PYEEIE-OH
A
6N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HUMAN SRC
B
107Homo sapiensGene Names: SRC (SRC1)
EC: 2.7.10.2
Find proteins for P12931 (Homo sapiens)
Go to Gene View: SRC
Go to UniProtKB:  P12931
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PTRΔG: -21.4 kJ/mol (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 23 
  • Olderado: 1HCT Olderado
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-09-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance