Biological Assembly 1  

 3D View: Structure | Electron Density | 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.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 302.26 kDa 
• Atom Count: 22131 
• Modelled Residue Count: 2702 
• Deposited 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, Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• 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: 2.30 Å
• R-Value Free: 0.215 
• R-Value Work: 0.179 
• R-Value Observed: 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:  
  3NIF, 3NIG, 3NID


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-IIb	A, C	457	Homo sapiens	Mutation(s): 0  Gene Names: ITGA2B, GP2B, ITGAB
Find proteins for P08514 (Homo sapiens) Explore P08514  Go to UniProtKB:  P08514
NIH Common Fund Data Resources
PHAROS:  P08514 GTEx:  ENSG00000005961

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-3	B, D	471	Homo sapiens	Mutation(s): 0  Gene Names: ITGB3, GP3A
Find proteins for P05106 (Homo sapiens) Explore P05106  Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS:  P05106 GTEx:  ENSG00000259207

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10E5 heavy chain	E, G [auth H]	221	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10E5 light chain	F, H [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	I [auth G]	5		N-Glycosylation

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], L [auth K]	2		N-Glycosylation

Entity ID: 7
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J]	3		N-Glycosylation

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth B], QA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	CA [auth B],  JA [auth C],  KA [auth C],  LA [auth C],  MA [auth C],  RA [auth D],  SA [auth D],  TA [auth H],  UA [auth L],  W [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	BA [auth B],  HA [auth C],  IA [auth C],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	DA [auth C],  EA [auth C],  FA [auth C],  GA [auth C],  M [auth A],  N [auth A],  O [auth A],  OA [auth D],  P [auth A],  PA [auth D],  Y [auth B],  Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	NA [auth D], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.215 
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 258.97	α = 90
b = 144.49	β = 90
c = 104.2	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary