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- PDB-5hgj: Structure of integrin alpha1beta1 and alpha2beta1 I-domains expla... -

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Basic information

Entry
Database: PDB / ID: 5hgj
TitleStructure of integrin alpha1beta1 and alpha2beta1 I-domains explain differential calcium-mediated ligand recognition
ComponentsIntegrin alpha-1
KeywordsCELL ADHESION / integrin / signaling / rossman / I-domain
Function / homology
Function and homology information


cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin ...cellular extravasation / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Other semaphorin interactions / CHL1 interactions / Laminin interactions / basal part of cell / Platelet Adhesion to exposed collagen / integrin complex / cell adhesion mediated by integrin / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of phosphoprotein phosphatase activity / Smooth Muscle Contraction / Integrin cell surface interactions / collagen binding / neutrophil chemotaxis / cell-matrix adhesion / neuron projection morphogenesis / acrosomal vesicle / integrin-mediated signaling pathway / cell-cell adhesion / vasodilation / positive regulation of neuron apoptotic process / integrin binding / perikaryon / protein phosphatase binding / positive regulation of MAPK cascade / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / 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 / SYNCHROTRON / Resolution: 1.399 Å
AuthorsBrown, K.L. / Banerjee, S. / Feigley, A. / Abe, H. / Blackwell, T. / Zent, R. / Pozzi, A. / Hudson, B.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL94296-06 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK018381 United States
CitationJournal: Sci Rep / Year: 2018
Title: Salt-bridge modulates differential calcium-mediated ligand binding to integrin alpha 1- and alpha 2-I domains.
Authors: Brown, K.L. / Banerjee, S. / Feigley, A. / Abe, H. / Blackwell, T.S. / Pozzi, A. / Hudson, B.G. / Zent, R.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-1
B: Integrin alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9216
Polymers43,7142
Non-polymers2084
Water8,287460
1
A: Integrin alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0244
Polymers21,8571
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integrin alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8972
Polymers21,8571
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.369, 95.950, 53.078
Angle α, β, γ (deg.)90.00, 104.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integrin alpha-1 / CD49 antigen-like family member A / Laminin and collagen receptor / VLA-1


Mass: 21856.754 Da / Num. of mol.: 2 / Fragment: Extracellular VWFA domain residues 170-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P56199
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Tris-HCl, Calcium Chloride, Sodium Chloride, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.36→150 Å / Num. obs: 67058 / % possible obs: 94.6 % / Redundancy: 3.6 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.399→47.975 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 3349 5 %
Rwork0.1776 --
obs0.1789 66995 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→47.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3047 0 9 460 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063135
X-RAY DIFFRACTIONf_angle_d1.0584241
X-RAY DIFFRACTIONf_dihedral_angle_d20.0411185
X-RAY DIFFRACTIONf_chiral_restr0.097497
X-RAY DIFFRACTIONf_plane_restr0.005548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3994-1.41940.31351090.28532078X-RAY DIFFRACTION74
1.4194-1.44060.28911370.26232587X-RAY DIFFRACTION90
1.4406-1.46310.29961370.25042591X-RAY DIFFRACTION93
1.4631-1.48710.2741380.23512638X-RAY DIFFRACTION93
1.4871-1.51270.24661400.21192656X-RAY DIFFRACTION95
1.5127-1.54020.24791390.20382661X-RAY DIFFRACTION94
1.5402-1.56990.2331380.20092618X-RAY DIFFRACTION93
1.5699-1.60190.22041410.19042692X-RAY DIFFRACTION96
1.6019-1.63670.22251400.19382657X-RAY DIFFRACTION94
1.6367-1.67480.22821440.18742730X-RAY DIFFRACTION97
1.6748-1.71670.21651410.18942697X-RAY DIFFRACTION95
1.7167-1.76310.21551420.18292705X-RAY DIFFRACTION97
1.7631-1.8150.23061410.18292678X-RAY DIFFRACTION95
1.815-1.87360.20591370.17892612X-RAY DIFFRACTION92
1.8736-1.94060.19571430.17342702X-RAY DIFFRACTION97
1.9406-2.01830.18121430.17862730X-RAY DIFFRACTION96
2.0183-2.11010.21931440.17772719X-RAY DIFFRACTION96
2.1101-2.22140.20591410.17952682X-RAY DIFFRACTION96
2.2214-2.36050.2171410.17482681X-RAY DIFFRACTION95
2.3605-2.54280.21751430.18022711X-RAY DIFFRACTION96
2.5428-2.79860.21221440.17792740X-RAY DIFFRACTION97
2.7986-3.20350.19561430.17422703X-RAY DIFFRACTION96
3.2035-4.03580.16011420.15072687X-RAY DIFFRACTION94
4.0358-48.00320.18471410.15952691X-RAY DIFFRACTION93

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