1OLZ

The ligand-binding face of the semaphorins revealed by the high resolution crystal structure of SEMA4D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Ligand-Binding Face of the Semaphorins Revealed by the High-Resolution Crystal Structure of Sema4D

Love, C.A.Harlos, K.Mavaddat, N.Davis, S.J.Stuart, D.I.Jones, E.Y.Esnouf, R.M.

(2003) Nat.Struct.Mol.Biol. 10: 843

  • DOI: 10.1038/nsb977

  • PubMed Abstract: 
  • Semaphorins, proteins characterized by an extracellular sema domain, regulate axon guidance, immune function and angiogenesis. The crystal structure of SEMA4D (residues 1-657) shows the sema topology to be a seven-bladed beta-propeller, revealing an ...

    Semaphorins, proteins characterized by an extracellular sema domain, regulate axon guidance, immune function and angiogenesis. The crystal structure of SEMA4D (residues 1-657) shows the sema topology to be a seven-bladed beta-propeller, revealing an unexpected homology with integrins. The sema beta-propeller contains a distinctive 77-residue insertion between beta-strands C and D of blade 5. Blade 7 is followed by a domain common to plexins, semaphorins and integrins (PSI domain), which forms a compact cysteine knot abutting the side of the propeller, and an Ig-like domain. The top face of the beta-propeller presents prominent loops characteristic of semaphorins. In addition to limited contact between the Ig-like domains, the homodimer is stabilized through extensive interactions between the top faces in a sector of the beta-propeller used for heterodimerization in integrins. This face of the propeller also mediates ligand binding in integrins, and functional data for semaphorin-receptor interactions map to the equivalent surface.


    Organizational Affiliation

    Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEMAPHORIN 4D
A, B
663Homo sapiensGene Names: SEMA4D (C9orf164, CD100, SEMAJ)
Find proteins for Q92854 (Homo sapiens)
Go to Gene View: SEMA4D
Go to UniProtKB:  Q92854
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.206 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 73.320α = 77.41
b = 76.760β = 73.35
c = 89.410γ = 63.57
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance