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- PDB-1aox: I DOMAIN FROM INTEGRIN ALPHA2-BETA1 -

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Basic information

Entry
Database: PDB / ID: 1aox
TitleI DOMAIN FROM INTEGRIN ALPHA2-BETA1
ComponentsINTEGRIN ALPHA 2 BETA
KeywordsINTEGRIN / CELL ADHESION / GLYCOPROTEIN
Function / homology
Function and homology information


collagen receptor activity / substrate-dependent cell migration / positive regulation of cell projection organization / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / response to L-ascorbic acid / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition ...collagen receptor activity / substrate-dependent cell migration / positive regulation of cell projection organization / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / response to L-ascorbic acid / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / CHL1 interactions / skin morphogenesis / Laminin interactions / positive regulation of smooth muscle contraction / collagen-activated signaling pathway / basal part of cell / positive regulation of phagocytosis, engulfment / Platelet Adhesion to exposed collagen / hepatocyte differentiation / mammary gland development / focal adhesion assembly / mesodermal cell differentiation / heparan sulfate proteoglycan binding / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / integrin complex / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / response to muscle activity / positive regulation of smooth muscle cell migration / cell-substrate adhesion / response to amine / 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 / laminin binding / collagen binding / axon terminus / extracellular matrix organization / positive regulation of cell adhesion / cell-matrix adhesion / positive regulation of translation / animal organ morphogenesis / integrin-mediated signaling pathway / female pregnancy / positive regulation of smooth muscle cell proliferation / cellular response to estradiol stimulus / cell-cell adhesion / cellular response to mechanical stimulus / blood coagulation / integrin binding / amyloid-beta binding / virus 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 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. ...: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEmsley, J. / King, S.L. / Bergelson, J.M. / Liddington, R.C.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Crystal structure of the I domain from integrin alpha2beta1.
Authors: Emsley, J. / King, S.L. / Bergelson, J.M. / Liddington, R.C.
History
DepositionJul 13, 1997Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRIN ALPHA 2 BETA
B: INTEGRIN ALPHA 2 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5294
Polymers44,4802
Non-polymers492
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.540, 43.290, 68.040
Angle α, β, γ (deg.)88.27, 76.59, 66.74
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6052, -0.7853, -0.1306), (-0.7944, 0.5848, 0.1643), (-0.0526, 0.2031, -0.9777)
Vector: 40.2061, 19.3848, 47.415)

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Components

#1: Protein INTEGRIN ALPHA 2 BETA


Mass: 22240.111 Da / Num. of mol.: 2 / Fragment: I DOMAIN / Mutation: T137R, Q138S, P139S, T338G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17301
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Emsley, J., (1997) J. Biol. Chem., 272, 28512.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
216-20 %PEG80001reservoir
350 mMHEPES1reservoir
410 mM1reservoirMgCl2
520 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23946 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.103 / Net I/σ(I): 21.8
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 9.7 / Rsym value: 0.259 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IDO

1ido


Resolution: 2.1→15 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.219 --
obs0.219 23946 99.5 %
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3006 0 2 83 3091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.16
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAMPCA.B72TOPHPCA.B72
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION4PARDNA.PROTOPDNA.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.47

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