Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 150.90 kDa 
• Atom Count: 10686 
• Modelled Residue Count: 1342 
• Deposited 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, Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• 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: 3.10 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

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:  
  2VC2, 2VDK, 2VDL, 2VDM, 2VDN, 2VDO, 2VDP, 2VDQ, 2VDR


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRIN ALPHA-IIB	A	452	Homo sapiens	Mutation(s): 0  Gene Names: ITGA2B, GP2B, ITGAB
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens) Explore P08514  Go to UniProtKB:  P08514
PHAROS:  P08514 GTEx:  ENSG00000005961

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRIN BETA-3	B	461	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3, GP3A
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens) Explore P05106  Go to UniProtKB:  P05106
PHAROS:  P05106 GTEx:  ENSG00000259207

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN	C [auth H]	221	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN	D [auth L]	214	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09609EN GlyCosmos:  G09609EN GlyGen:  G09609EN

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
180 (Subject of Investigation/LOI)	O [auth B]	2-(S)-[N-(3-PYRIDYLSULFONYL)AMINO]-3-[[2-CARBONYL-5-[2-(PIPERIDIN-4-YL)ETHYL]-THIENO[2,3-B]THIOPHENEYL]AMINO]-PROPIONIC ACID C22 H26 N4 O5 S3 QDIFCBMBPLLNGR-GOSISDBHSA-N
NAG (Subject of Investigation/LOI)	M [auth A], N [auth A], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	H [auth A], P [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	G [auth A], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
180	BindingDB:  2VC2	Kd: min: 0.07, max: 28 (nM) from 2 assay(s)
		IC50: min: 8, max: 19 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.217 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.151	α = 90
b = 149.151	β = 90
c = 176.217	γ = 120

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Refinement description, Version format compliance
• Version 1.2: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-11-20
  Changes: Advisory, Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary