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- PDB-9vb8: Crystal structure of human integrin alpha2 I domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9vb8
TitleCrystal structure of human integrin alpha2 I domain in complex with homo-trimeric collagen model peptide.
Components
  • Collagen model peptide
  • Integrin alpha-2
KeywordsCELL ADHESION / Integrin / collagen
Function / homology
Function and homology information


collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / skin morphogenesis ...collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / positive regulation of cell projection organization / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / skin morphogenesis / CHL1 interactions / response to L-ascorbic acid / collagen-activated signaling pathway / positive regulation of smooth muscle contraction / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / hepatocyte differentiation / positive regulation of phagocytosis, engulfment / focal adhesion assembly / mammary gland development / heparan sulfate proteoglycan binding / mesodermal cell differentiation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / response to amine / integrin complex / cell adhesion mediated by integrin / MET activates PTK2 signaling / positive regulation of smooth muscle cell migration / Syndecan interactions / response to muscle activity / cell-substrate adhesion / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / ECM proteoglycans / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / collagen binding / extracellular matrix organization / laminin binding / positive regulation of cell adhesion / positive regulation of smooth muscle cell proliferation / axon terminus / animal organ morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / positive regulation of translation / cellular response to estradiol stimulus / female pregnancy / cellular response to mechanical stimulus / cell-cell adhesion / integrin binding / blood coagulation / amyloid-beta binding / virus receptor activity / signaling receptor activity / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). ...: / Integrin alpha Ig-like domain 3 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsShibata, S. / Oki, H. / Kawahara, K. / Masuda, R. / Fujii, K. / Koide, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJSP2128 Japan
CitationJournal: To Be Published
Title: A cryptic interaction mode between the collagen triple helix and integrin alpha2beta1 unveiled through ligands obtained from a random peptide library
Authors: Shibata, S. / Oki, H. / Kawahara, K. / Masuda, R. / Fujii, K. / Koide, T.
History
DepositionJun 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-2
B: Collagen model peptide
C: Collagen model peptide
D: Collagen model peptide
E: Integrin alpha-2
F: Collagen model peptide
G: Collagen model peptide
H: Collagen model peptide
I: Integrin alpha-2
J: Collagen model peptide
K: Collagen model peptide
L: Collagen model peptide
M: Integrin alpha-2
N: Collagen model peptide
O: Collagen model peptide
P: Collagen model peptide


Theoretical massNumber of molelcules
Total (without water)114,64116
Polymers114,64116
Non-polymers00
Water27,1131505
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32740 Å2
ΔGint-161 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.364, 71.764, 83.861
Angle α, β, γ (deg.)110.280, 90.090, 112.210
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha


Mass: 21734.537 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301
#2: Protein/peptide
Collagen model peptide


Mass: 2308.530 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1505 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium acetate, 0.1M sodium acetate buffer pH 4.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48.67 Å / Num. obs: 153836 / % possible obs: 96.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 19.19 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.093 / Rrim(I) all: 0.153 / Χ2: 0.59 / Net I/σ(I): 4.7 / Num. measured all: 346318
Reflection shellResolution: 1.6→1.63 Å / % possible obs: 94.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.552 / Num. measured all: 16776 / Num. unique obs: 7439 / CC1/2: 0.508 / Rpim(I) all: 0.438 / Rrim(I) all: 0.708 / Χ2: 0.29 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.67 Å / SU ML: 0.2235 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.7504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2223 15462 10.05 %
Rwork0.1852 138357 -
obs0.1889 153819 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.19 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8036 0 48 1505 9589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778505
X-RAY DIFFRACTIONf_angle_d1.061111620
X-RAY DIFFRACTIONf_chiral_restr0.06191273
X-RAY DIFFRACTIONf_plane_restr0.00791526
X-RAY DIFFRACTIONf_dihedral_angle_d15.10453062
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.36094920.32374535X-RAY DIFFRACTION93.96
1.62-1.640.34215140.29654522X-RAY DIFFRACTION94.54
1.64-1.660.31715190.29124456X-RAY DIFFRACTION94.85
1.66-1.680.28874590.26154613X-RAY DIFFRACTION95.02
1.68-1.70.30355110.24174523X-RAY DIFFRACTION95.32
1.7-1.720.26275130.22064612X-RAY DIFFRACTION95.33
1.72-1.750.2515080.21384556X-RAY DIFFRACTION95.26
1.75-1.770.25975140.21264548X-RAY DIFFRACTION95.22
1.77-1.80.2645160.20614493X-RAY DIFFRACTION95.45
1.8-1.830.24625270.19794607X-RAY DIFFRACTION96.12
1.83-1.860.25435170.20654588X-RAY DIFFRACTION95.87
1.86-1.90.25555060.20934605X-RAY DIFFRACTION96.11
1.9-1.930.27184770.24414608X-RAY DIFFRACTION96.29
1.93-1.970.25385290.21534539X-RAY DIFFRACTION95.77
1.97-2.020.22474570.19174681X-RAY DIFFRACTION96.43
2.02-2.060.23165220.19354660X-RAY DIFFRACTION96.95
2.06-2.110.22064920.18754618X-RAY DIFFRACTION96.58
2.11-2.170.21825500.1794632X-RAY DIFFRACTION97.06
2.17-2.240.21135140.17854660X-RAY DIFFRACTION97.26
2.24-2.310.23015300.18794631X-RAY DIFFRACTION97.07
2.31-2.390.2394840.18494688X-RAY DIFFRACTION97.35
2.39-2.490.22235370.18384588X-RAY DIFFRACTION96.81
2.49-2.60.21494860.18054679X-RAY DIFFRACTION97.56
2.6-2.740.21615990.17944577X-RAY DIFFRACTION97.09
2.74-2.910.22615150.18014679X-RAY DIFFRACTION98.04
2.91-3.130.21735270.18074725X-RAY DIFFRACTION98.22
3.13-3.450.21645300.17254663X-RAY DIFFRACTION98.26
3.45-3.950.19675210.16024656X-RAY DIFFRACTION97.39
3.95-4.970.17585510.14414700X-RAY DIFFRACTION98.72
4.97-48.670.19525450.17834715X-RAY DIFFRACTION98.93

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