3VI4

Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide

• PDB DOI: https://doi.org/10.2210/pdb3VI4/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: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 339.88 kDa 
• Atom Count: 22,882 
• Modelled Residue Count: 2,935 
• Deposited Residue Count: 3,056 
• Unique protein chains: 5

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
UniProt & NIH Common Fund Data Resources
Find proteins for P08648 (Homo sapiens) Explore P08648  Go to UniProtKB:  P08648
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
UniProt & NIH Common Fund Data Resources
Find proteins for P05556 (Homo sapiens) Explore P05556  Go to UniProtKB:  P05556
PHAROS:  P05556 GTEx:  ENSG00000150093

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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SG/19 Fab fragment (Heavy chain)	F [auth H], H [auth F]	218	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RGD peptide	I [auth G], J [auth I]	5	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth J], M	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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-glucopyranose	L [auth K], N	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G09724ZC GlyCosmos:  G09724ZC GlyGen:  G09724ZC

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	EA [auth C], FA [auth C], GA [auth C], HA [auth C], KA [auth D], S [auth A], T [auth A], U [auth A], V [auth A], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	AA [auth C], BA [auth C], CA [auth C], DA [auth C], IA [auth D], O [auth A], P [auth A], Q [auth A], R [auth A], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	JA [auth D], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.805	α = 75.72
b = 103.869	β = 70.16
c = 125.262	γ = 70.9

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

• 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: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary