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: 2.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 Biol 10: 843

  • DOI: 10.1038/nsb977
  • Primary Citation of Related Structures:  
    1OLZ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEMAPHORIN 4DAB663Homo sapiensMutation(s): 0 
Gene Names: SEMA4DC9orf164CD100SEMAJ
Find proteins for Q92854 (Homo sapiens)
Explore Q92854 
Go to UniProtKB:  Q92854
NIH Common Fund Data Resources
PHAROS  Q92854
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.32α = 77.41
b = 76.76β = 73.35
c = 89.41γ = 63.57
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Source and taxonomy