3FCS

Structure of complete ectodomain of integrin aIIBb3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structure of a complete integrin ectodomain in a physiologic resting state and activation and deactivation by applied forces.

Zhu, J.Luo, B.H.Xiao, T.Zhang, C.Nishida, N.Springer, T.A.

(2008) Mol Cell 32: 849-861

  • DOI: 10.1016/j.molcel.2008.11.018
  • Primary Citation of Related Structures:  
    3FCS, 3FCU

  • PubMed Abstract: 
  • The complete ectodomain of integrin alpha(IIb)beta(3) reveals a bent, closed, low-affinity conformation, the beta knee, and a mechanism for linking cytoskeleton attachment to high affinity for ligand. Ca and Mg ions in the recognition site, including the synergistic metal ion binding site (SyMBS), are loaded prior to ligand binding ...

    The complete ectodomain of integrin alpha(IIb)beta(3) reveals a bent, closed, low-affinity conformation, the beta knee, and a mechanism for linking cytoskeleton attachment to high affinity for ligand. Ca and Mg ions in the recognition site, including the synergistic metal ion binding site (SyMBS), are loaded prior to ligand binding. Electrophilicity of the ligand-binding Mg ion is increased in the open conformation. The beta(3) knee passes between the beta(3)-PSI and alpha(IIb)-knob to bury the lower beta leg in a cleft, from which it is released for extension. Different integrin molecules in crystals and EM reveal breathing that appears on pathway to extension. Tensile force applied to the extended ligand-receptor complex stabilizes the closed, low-affinity conformation. By contrast, an additional lateral force applied to the beta subunit to mimic attachment to moving actin filaments stabilizes the open, high-affinity conformation. This mechanism propagates allostery over long distances and couples cytoskeleton attachment of integrins to their high-affinity state.


    Organizational Affiliation

    The Immune Disease Institute and Department of Pathology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin, alpha 2bA, C959Homo sapiensMutation(s): 0 
Gene Names: ITGA2BGP2BITGAB
UniProt & NIH Common Fund Data Resources
Find proteins for P08514 (Homo sapiens)
Explore P08514 
Go to UniProtKB:  P08514
PHAROS:  P08514
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-3B, D690Homo sapiensMutation(s): 1 
Gene Names: ITGB3GP3A
UniProt & NIH Common Fund Data Resources
Find proteins for P05106 (Homo sapiens)
Explore P05106 
Go to UniProtKB:  P05106
PHAROS:  P05106
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, H, J, K, L, M, N2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseF4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G48068RF
GlyCosmos:  G48068RF
GlyGen:  G48068RF
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-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-glucopyranoseI5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G75436UI
GlyCosmos:  G75436UI
GlyGen:  G75436UI
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth C], FA [auth C], OA [auth D], T [auth A], U [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], V [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , MA [auth D] , NA [auth D] , O [auth A] , P [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  MA [auth D],  NA [auth D],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  X [auth B],  Y [auth B],  Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
LA [auth D], W [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.3α = 90
b = 81.3β = 90
c = 654.623γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary