3VI3

Crystal structure of alpha5beta1 integrin headpiece (ligand-free form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor

Nagae, M.Re, S.Mihara, E.Nogi, T.Sugita, Y.Takagi, J.

(2012) J Cell Biol 197: 131-140

  • DOI: 10.1083/jcb.201111077
  • Primary Citation of Related Structures:  
    3VI3, 3VI4

  • PubMed Abstract: 
  • Integrin α5β1 is a major cellular receptor for the extracellular matrix protein fibronectin and plays a fundamental role during mammalian development. A crystal structure of the α5β1 integrin headpiece fragment bound by an allosteric inhibitory antibody was determined at a 2 ...

    Integrin α5β1 is a major cellular receptor for the extracellular matrix protein fibronectin and plays a fundamental role during mammalian development. A crystal structure of the α5β1 integrin headpiece fragment bound by an allosteric inhibitory antibody was determined at a 2.9-Å resolution both in the absence and presence of a ligand peptide containing the Arg-Gly-Asp (RGD) sequence. The antibody-bound β1 chain accommodated the RGD ligand with very limited structural changes, which may represent the initial step of cell adhesion mediated by nonactivated integrins. Furthermore, a molecular dynamics simulation pointed to an important role for Ca(2+) in the conformational coupling between the ligand-binding site and the rest of the molecule. The RGD-binding pocket is situated at the center of a trenchlike exposed surface on the top face of α5β1 devoid of glycosylation sites. The structure also enabled the precise prediction of the acceptor residue for the auxiliary synergy site of fibronectin on the α5 subunit, which was experimentally confirmed by mutagenesis and kinetic binding assays.


    Organizational Affiliation

    Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin alpha-5A, C632Homo sapiensMutation(s): 0 
Gene Names: FNRAITGA5
UniProt & NIH Common Fund Data Resources
Find proteins for P08648 (Homo sapiens)
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Go to UniProtKB:  P08648
PHAROS:  P08648
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Integrin beta-1B, D454Homo sapiensMutation(s): 0 
Gene Names: FNRBITGB1MDF2MSK12
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens)
Explore P05556 
Go to UniProtKB:  P05556
PHAROS:  P05556
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SG/19 Fab fragment (Light chain)G [auth E], E [auth L]219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SG/19 Fab fragment (Heavy chain)H [auth F], F [auth H]218Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G], L [auth K]6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I], K [auth J]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
DA [auth C] , EA [auth C] , FA [auth C] , GA [auth C] , KA [auth D] , Q [auth A] , R [auth A] , S [auth A] , 
DA [auth C],  EA [auth C],  FA [auth C],  GA [auth C],  KA [auth D],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , HA [auth D] , IA [auth D] , M [auth A] , N [auth A] , O [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  HA [auth D],  IA [auth D],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  V [auth B],  W [auth B],  Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.956α = 76.1
b = 102.805β = 70.19
c = 125.079γ = 71.28
Software Package:
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary