Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 148.63 kDa 
• Atom Count: 10669 
• Modelled Residue Count: 1244 
• Deposited Residue Count: 1326 
• Unique protein chains: 1

1OLZ

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

• PDB DOI: 10.2210/pdb1OLZ/pdb

• Classification: DEVELOPMENTAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2003-08-19 Released: 2003-09-11 
• Deposition Author(s): Love, C.A., Harlos, K., Mavaddat, N., Davis, S.J., Stuart, D.I., Jones, E.Y., Esnouf, R.M.

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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 

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

• PubMed: 12958590 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEMAPHORIN 4D	A, B	663	Homo sapiens	Mutation(s): 0  Gene Names: SEMA4D, C9orf164, CD100, SEMAJ
UniProt & NIH Common Fund Data Resources
Find proteins for Q92854 (Homo sapiens) Explore Q92854  Go to UniProtKB:  Q92854
PHAROS:  Q92854

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 = 73.32	α = 77.41
b = 76.76	β = 73.35
c = 89.41	γ = 63.57

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-19 
• Released Date: 2003-09-11 
Deposition Author(s): Love, C.A., Harlos, K., Mavaddat, N., Davis, S.J., Stuart, D.I., Jones, E.Y., Esnouf, R.M.

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