1B4F | pdb_00001b4f

OLIGOMERIC STRUCTURE OF THE HUMAN EPHB2 RECEPTOR SAM DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1B4F/pdb

• Classification: SIGNAL TRANSDUCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-12-20 Released: 1999-02-16 
• Deposition Author(s): Thanos, C.D., Goodwill, K.E., Bowie, J.U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.273 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Oligomeric structure of the human EphB2 receptor SAM domain.

Thanos, C.D., Goodwill, K.E., Bowie, J.U.

(1999) Science 283: 833-836

• PubMed: 9933164 
• DOI: https://doi.org/10.1126/science.283.5403.833
• Primary Citation Related Structures: 
  1B4F


• PubMed Abstract: 
  

  The sterile alpha motif (SAM) domain is a protein interaction module that is present in diverse signal-transducing proteins. SAM domains are known to form homo- and hetero-oligomers. The crystal structure of the SAM domain from an Eph receptor tyrosine kinase, EphB2, reveals two large interfaces. In one interface, adjacent monomers exchange amino-terminal peptides that insert into a hydrophobic groove on each neighbor. A second interface is composed of the carboxyl-terminal helix and a nearby loop. A possible oligomer, constructed from a combination of these binding modes, may provide a platform for the formation of larger protein complexes.

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Organizational Affiliation: 
• UCLA-DOE Laboratory of Structural Biology and Molecular Medicine and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.21 kDa 
• Atom Count: 5,564 
• Modeled Residue Count: 599 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHB2	A, B, C, D, E, F, G, H	82	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29323 (Homo sapiens) Explore P29323  Go to UniProtKB:  P29323
PHAROS:  P29323 GTEx:  ENSG00000133216

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.273 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.897	α = 90
b = 73.897	β = 90
c = 104.547	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SHAKE-N-BAKE	model building
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing
SHAKE-N-BAKE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Thanos, C.D., Goodwill, K.E., Bowie, J.U.

Revision History  

• Version 1.0: 1999-02-16
  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: 2019-12-11
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references