Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 298.45 kDa 
• Atom Count: 21019 
• Residue Count: 2676 
• Unique protein chains: 2

1TYE

Structural basis for allostery in integrins and binding of ligand-mimetic therapeutics to the platelet receptor for fibrinogen

• DOI: 10.2210/pdb1TYE/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2004-07-07 Released: 2004-10-12 
• Deposition Author(s): Xiao, T., Takagi, J., Coller, B.S., Wang, J.-H., Springer, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.254 
• R-Value Work: 0.219 
• R-Value Observed: 0.268 

Literature

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: 59-67

• PubMed: 15378069 
• DOI: 10.1038/nature02976
• Primary Citation of Related Structures:  
  1TYE


• PubMed Abstract: 
  

Integrins are important adhesion receptors in all Metazoa that transmit conformational change bidirectionally across the membrane. Integrin alpha and beta subunits form a head and two long legs in the ectodomain and span the membrane. Here, we define with crystal structures the atomic basis for allosteric regulation of the conformation and affinity for ligand of the integrin ectodomain, and how fibrinogen-mimetic therapeutics bind to platelet integrin alpha(IIb)beta3. Allostery in the beta3 I domain alters three metal binding sites, associated loops and alpha1- and alpha7-helices. Piston-like displacement of the alpha7-helix causes a 62 degrees reorientation between the beta3 I and hybrid domains. Transmission through the rigidly connected plexin/semaphorin/integrin (PSI) domain in the upper beta3 leg causes a 70 A separation between the knees of the alpha and beta legs. Allostery in the head thus disrupts interaction between the legs in a previously described low-affinity bent integrin conformation, and leg extension positions the high-affinity head far above the cell surface.

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Organizational Affiliation: 

The CBR Institute for Biomedical Research and Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-IIb	A, C, E	452	Homo sapiens	Mutation(s): 0  Gene Names: ITGAB, ITGA2B, GP2B
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, F	440	Homo sapiens	Mutation(s): 0  Gene Names: ITGAB, ITGB3, GP3A
Find proteins for P05106 (Homo sapiens) Explore P05106  Go to UniProtKB:  P05106
NIH Common Fund Data Resources
PHAROS:  P05106 GTEx:  ENSG00000259207

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-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	G, I	4		N-Glycosylation

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-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	H	5		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B, D, E, F	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CAC	B, D, F	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA	A, B, C, D, E, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B, D, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.254 
• R-Value Work: 0.219 
• R-Value Observed: 0.268 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 332.093	α = 90
b = 332.093	β = 90
c = 88.288	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-07 
• Released Date: 2004-10-12 
Deposition Author(s): Xiao, T., Takagi, J., Coller, B.S., Wang, J.-H., Springer, T.A.

Revision History 

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-09-10
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary