Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 302399.56 
• Atom Count: 21072 
• Residue Count: 2726 
• Unique protein chains: 4

3NID

The Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3 -Specific Antagonist That Does Not Induce Opening

• DOI: 10.2210/pdb3NID/pdb

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


• Deposited: 2010-06-15 Released: 2010-12-22 
• Deposition Author(s): Zhu, J.H., Zhu, J.Q., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.215 
• R-Value Work: 0.179 

Literature

Closed headpiece of integrin {alpha}IIb{beta}3 and its complex with an {alpha}IIb{beta}3-specific antagonist that does not induce opening.

Zhu, J.H., Zhu, J.Q., Negri, A., Provasi, D., Filizola, M., Coller, B.S., Springer, T.A.

(2010) Blood 116: 5050-5059

• PubMed: 20679525 
• DOI: 10.1182/blood-2010-04-281154
• Primary Citation of Related Structures:  
  3NIG, 3NIF


• PubMed Abstract: 
  

The platelet integrin α(IIb)β(3) is essential for hemostasis and thrombosis through its binding of adhesive plasma proteins. We have determined crystal structures of the α(IIb)β(3) headpiece in the absence of ligand and after soaking in RUC-1, a novel small molecule antagonist. In the absence of ligand, the α(IIb)β(3) headpiece is in a closed conformation, distinct from the open conformation visualized in presence of Arg-Gly-Asp (RGD) antagonists. In contrast to RGD antagonists, RUC-1 binds only to the α(IIb) subunit. Molecular dynamics revealed nearly identical binding. Two species-specific residues, α(IIb) Y190 and α(IIb) D232, in the RUC-1 binding site were confirmed as important by mutagenesis. In sharp contrast to RGD-based antagonists, RUC-1 did not induce α(IIb)β(3) to adopt an open conformation, as determined by gel filtration and dynamic light scattering. These studies provide insights into the factors that regulate integrin headpiece opening, and demonstrate the molecular basis for a novel mechanism of integrin antagonism.

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Organizational Affiliation: 

Immune Disease Institute, Children's Hospital Boston, and Department of Pathology, 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, C	457	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, D	471	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	E, 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	F, 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
SO4	A, B, C, D, H, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	B, D	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
MG	B, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NAG	B, D	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.215 
• R-Value Work: 0.179 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 258.970	α = 90.00
b = 144.490	β = 90.00
c = 104.200	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
Blu-Ice	data collection
XDS	data scaling
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-06-15 
• Released Date: 2010-12-22 
• Deposition Author(s): Zhu, J.H., Zhu, J.Q., Springer, T.A.

Revision History 

• Version 1.0: 2010-12-22
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance