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- PDB-4bj3: Integrin alpha2 I domain E318W-collagen complex -

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Basic information

Entry
Database: PDB / ID: 4bj3
TitleIntegrin alpha2 I domain E318W-collagen complex
Components
  • GFOGER PEPTIDE
  • INTEGRIN ALPHA-2
KeywordsCELL ADHESION
Function / homology
Function and homology information


collagen type XXVI trimer / collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / Collagen chain trimerization / hypotonic response ...collagen type XXVI trimer / collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / Collagen chain trimerization / hypotonic response / response to L-ascorbic acid / Collagen biosynthesis and modifying enzymes / CHL1 interactions / skin morphogenesis / Laminin interactions / positive regulation of phagocytosis, engulfment / basal part of cell / positive regulation of smooth muscle contraction / collagen-activated signaling pathway / mammary gland development / Platelet Adhesion to exposed collagen / hepatocyte differentiation / mesodermal cell differentiation / focal adhesion assembly / heparan sulfate proteoglycan binding / positive regulation of cell-substrate adhesion / positive regulation of positive chemotaxis / response to muscle activity / integrin complex / positive regulation of leukocyte migration / cell adhesion mediated by integrin / MET activates PTK2 signaling / Syndecan interactions / positive regulation of epithelial cell migration / cell-substrate adhesion / positive regulation of smooth muscle cell migration / response to amine / Collagen degradation / positive regulation of collagen biosynthetic process / ECM proteoglycans / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / laminin binding / axon terminus / collagen binding / positive regulation of cell adhesion / extracellular matrix organization / cell-matrix adhesion / cellular response to estradiol stimulus / integrin-mediated signaling pathway / female pregnancy / positive regulation of translation / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / cell-cell adhesion / cellular response to mechanical stimulus / blood coagulation / integrin binding / virus receptor activity / amyloid-beta binding / collagen-containing extracellular matrix / response to hypoxia / cell adhesion / response to xenobiotic stimulus / endoplasmic reticulum lumen / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
EMI domain / EMI domain / EMI domain profile. / : / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Integrin alpha chain ...EMI domain / EMI domain / EMI domain profile. / : / : / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / 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
Integrin alpha-2 / Collagen alpha-1(XXVI) chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.042 Å
AuthorsCarafoli, F. / Hamaia, S.W. / Bihan, D. / Hohenester, E. / Farndale, R.W.
CitationJournal: Plos One / Year: 2013
Title: An Activating Mutation Reveals a Second Binding Mode of the Integrin Alpha2 I Domain to the Gfoger Motif in Collagens.
Authors: Carafoli, F. / Hamaia, S.W. / Bihan, D. / Hohenester, E. / Farndale, R.W.
History
DepositionApr 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Source and taxonomy
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTEGRIN ALPHA-2
B: INTEGRIN ALPHA-2
C: GFOGER PEPTIDE
D: GFOGER PEPTIDE
E: GFOGER PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6139
Polymers56,3205
Non-polymers2934
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-37.6 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.004, 83.004, 175.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 / CD49B


Mass: 25137.396 Da / Num. of mol.: 2 / Fragment: I DOMAIN, RESIDUES 171-368 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PDEST-N110 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ORIGAMI / References: UniProt: P17301
#2: Protein/peptide GFOGER PEPTIDE


Mass: 2015.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q96A83*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
Sequence detailsN-TERMINAL HIS-TAG AND E318W MUTATION SYNTHETIC PEPTIDE, O IS HYDROXYPROLINE

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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: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.04→29.35 Å / Num. obs: 12365 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 84.69 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.2
Reflection shellResolution: 3.04→3.25 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.9 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DZI

1dzi


Resolution: 3.042→29.346 Å / SU ML: 0.44 / σ(F): 1.91 / Phase error: 33.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1264 10.39 %
Rwork0.2457 --
obs0.251 12287 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.042→29.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 17 0 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033251
X-RAY DIFFRACTIONf_angle_d0.6534417
X-RAY DIFFRACTIONf_dihedral_angle_d11.871170
X-RAY DIFFRACTIONf_chiral_restr0.042502
X-RAY DIFFRACTIONf_plane_restr0.002568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0418-3.16340.41441180.35021132X-RAY DIFFRACTION94
3.1634-3.30720.3671410.31431199X-RAY DIFFRACTION100
3.3072-3.48130.37851380.30171202X-RAY DIFFRACTION100
3.4813-3.6990.34871430.27031206X-RAY DIFFRACTION100
3.699-3.9840.33581260.2461230X-RAY DIFFRACTION100
3.984-4.38370.33661530.22571218X-RAY DIFFRACTION100
4.3837-5.01540.26511440.21831228X-RAY DIFFRACTION100
5.0154-6.30850.27461490.25511253X-RAY DIFFRACTION100
6.3085-29.34770.2471520.22251355X-RAY DIFFRACTION100

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