Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

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

Macromolecule Content

• Total Structure Weight: 151084.83 
• Atom Count: 10588 
• Residue Count: 1348 
• Unique protein chains: 4

2VC2

Re-refinement of Integrin AlphaIIbBeta3 Headpiece Bound to Antagonist L-739758

• DOI: 10.2210/pdb2VC2/pdb
• Entry 2VC2 supersedes 1TY7

• Classification: CELL ADHESION/IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus


• Deposited: 2007-09-18 Released: 2008-09-02 
• Deposition Author(s): Springer, T.A., Zhu, J., Xiao, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 

Literature

Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3.

Springer, T.A., Zhu, J., Xiao, T.

(2008) J.Cell Biol. 182: 791

• PubMed: 18710925 
• DOI: 10.1083/jcb.200801146
• Primary Citation of Related Structures:  
  2VDR, 2VDQ, 2VDP, 2VDO, 2VDN, 2VDM, 2VDL, 2VDK


• PubMed Abstract: 
  

Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin alpha(IIb)beta(3) on platelets, resulting in platelet aggregation. alpha(v)beta(3) binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's alpha subunit. alpha(IIb)beta(3) also binds to fibrinogen; however, it does so via an unstructured RGD-lacking C-terminal region of the gamma subunit (gammaC peptide). These distinct modes of fibrinogen binding enable alpha(IIb)beta(3) and alpha(v)beta(3) to function cooperatively in hemostasis. In this study, crystal structures reveal the integrin alpha(IIb)beta(3)-gammaC peptide interface, and, for comparison, integrin alpha(IIb)beta(3) bound to a lamprey gammaC primordial RGD motif. Compared with RGD, the GAKQAGDV motif in gammaC adopts a different backbone configuration and binds over a more extended region. The integrin metal ion-dependent adhesion site (MIDAS) Mg(2+) ion binds the gammaC Asp side chain. The adjacent to MIDAS (ADMIDAS) Ca(2+) ion binds the gammaC C terminus, revealing a contribution for ADMIDAS in ligand binding. Structural data from this natively disordered gammaC peptide enhances our understanding of the involvement of gammaC peptide and integrin alpha(IIb)beta(3) in hemostasis and thrombosis.

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Related Citations: 

• Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics
  Xiao, T.,Takagi, J.,Coller, B.S.,Wang, J.-H.,Springer, T.A.
  (2004) Nature 432: 59




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Organizational Affiliation: 

Department of Pathology, Immune Disease Institute, Harvard Medical School, Boston, MA 02115, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
INTEGRIN ALPHA-IIB	A	452	Homo sapiens	Mutation(s): 0  Gene Names: ITGA2B (GP2B, ITGAB)
Find proteins for P08514 (Homo sapiens) Go to Gene View: ITGA2B Go to UniProtKB:  P08514

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
INTEGRIN BETA-3	B	461	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3 (GP3A)
Find proteins for P05106 (Homo sapiens) Go to Gene View: ITGB3 Go to UniProtKB:  P05106

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN	H	221	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN	L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	B	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
180	B	2-(S)-[N-(3-PYRIDYLSULFONYL)AMINO]-3-[[2-CARBONYL-5-[2-(PIPERIDIN-4-YL)ETHYL]-THIENO[2,3-B]THIOPHENEYL]AMINO]-PROPIONIC ACID MERCK L739758 C22 H26 N4 O5 S3 QDIFCBMBPLLNGR-GOSISDBHSA-N
NAG	A, B	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
180	IC50: 8 - 19 nM (100) BINDINGDB
180	Kd: 0.1 - 28 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 149.151	α = 90.00
b = 149.151	β = 90.00
c = 176.217	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-09-18 
• Released Date: 2008-09-02 
• Deposition Author(s): Springer, T.A., Zhu, J., Xiao, T.
• This entry supersedes: 1TY7

Revision History 

• Version 1.0: 2008-09-02
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Refinement description, Version format compliance
• Version 1.2: 2019-01-30
  Type: Data collection, Experimental preparation, Other
• Version 1.3: 2019-02-06
  Type: Data collection, Experimental preparation