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)

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 303966.75 
• Atom Count: 21197 
• Residue Count: 2740 
• Unique protein chains: 5

3ZDY

Integrin alphaIIB beta3 headpiece and RGD peptide complex

• DOI: 10.2210/pdb3ZDY/pdb

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


• Deposited: 2012-12-03 Released: 2013-06-05 
• Deposition Author(s): Zhu, J.H., Zhu, J.Q., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 

Literature

Complete Integrin Headpiece Opening in Eight Steps.

Zhu, J., Zhu, J., Springer, T.A.

(2013) J.Cell Biol. 201: 1053

• PubMed: 23798730 
• DOI: 10.1083/jcb.201212037
• Primary Citation of Related Structures:  
  3ZE2, 3ZE1, 3ZE0, 3ZDZ, 3ZDX


• PubMed Abstract: 
  

Carefully soaking crystals with Arg-Gly-Asp (RGD) peptides, we captured eight distinct RGD-bound conformations of the αIIbβ3 integrin headpiece. Starting from the closed βI domain conformation, we saw six intermediate βI conformations and finally the fully open βI with the hybrid domain swung out in the crystal lattice. The β1-α1 backbone that hydrogen bonds to the Asp side chain of RGD was the first element to move followed by adjacent to metal ion-dependent adhesion site Ca(2+), α1 helix, α1' helix, β6-α7 loop, α7 helix, and hybrid domain. We define in atomic detail how conformational change was transmitted over long distances in integrins, 40 Å from the ligand binding site to the opposite end of the βI domain and 80 Å to the far end of the hybrid domain. During these movements, RGD slid in its binding groove toward αIIb, and its Arg side chain became ordered. RGD concentration requirements in soaking suggested a >200-fold higher affinity after opening. The thermodynamic cycle shows how higher affinity pays the energetic cost of opening.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Program in Cellular and Molecular Medicine, Children's Hospital Boston, 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	472	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
10E5 FAB 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
10E5 FAB LIGHT CHAIN	F, L	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
RGD PEPTIDE	I, J	6	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, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	B, D	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	B, D	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-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: 2.45 Å
• R-Value Free: 0.216 
• R-Value Work: 0.182 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 257.760	α = 90.00
b = 145.250	β = 90.00
c = 106.060	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-03 
• Released Date: 2013-06-05 
• Deposition Author(s): Zhu, J.H., Zhu, J.Q., Springer, T.A.

Revision History 

• Version 1.0: 2013-06-05
  Type: Initial release
• Version 1.1: 2013-07-10
  Type: Database references
• Version 2.0: 2017-10-25
  Type: Advisory, Atomic model, Derived calculations