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: 338.85 kDa 
• Atom Count: 22803 
• Residue Count: 2923 
• Unique protein chains: 4

3VI3

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

• DOI: 10.2210/pdb3VI3/pdb

• Classification: CELL ADHESION/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Cricetulus griseus, Mus musculus
• Mutation(s): No 


• Deposited: 2011-09-21 Released: 2012-02-22 
• Deposition Author(s): Nagae, M., Nogi, T., Takagi, J.

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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 

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

• PubMed: 22451694 
• 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 2.9-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin alpha-5	A, C	632	Homo sapiens	Mutation(s): 0  Gene Names: FNRA, ITGA5
Find proteins for P08648 (Homo sapiens) Explore P08648  Go to UniProtKB:  P08648
NIH Common Fund Data Resources
PHAROS  P08648 GTEx  ENSG00000161638

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrin beta-1	B, D	454	Homo sapiens	Mutation(s): 0  Gene Names: FNRB, ITGB1, MDF2, MSK12
Find proteins for P05556 (Homo sapiens) Explore P05556  Go to UniProtKB:  P05556
NIH Common Fund Data Resources
PHAROS  P05556 GTEx  ENSG00000150093

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SG/19 Fab fragment (Light chain)	E, L	219	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SG/19 Fab fragment (Heavy chain)	F, H	218	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-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, K	6		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	I, J	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, D	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	B, D	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 92.956	α = 76.1
b = 102.805	β = 70.19
c = 125.079	γ = 71.28

Software Package:

Software Name	Purpose
SERGUI	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-21 
• Released Date: 2012-02-22 
Deposition Author(s): Nagae, M., Nogi, T., Takagi, J.

Revision History 

• 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