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- PDB-5hj2: Integrin alpha2beta1 I-domain -

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Basic information

Entry
Database: PDB / ID: 5hj2
TitleIntegrin alpha2beta1 I-domain
ComponentsIntegrin alpha-2
KeywordsCELL ADHESION / Adhesion / signaling
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 / positive regulation of smooth muscle contraction ...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 / positive regulation of smooth muscle contraction / skin morphogenesis / CHL1 interactions / response to L-ascorbic acid / basal part of cell / collagen-activated signaling pathway / positive regulation of phagocytosis, engulfment / Laminin interactions / hepatocyte differentiation / Platelet Adhesion to exposed collagen / focal adhesion assembly / mammary gland development / heparan sulfate proteoglycan binding / mesodermal cell differentiation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / integrin complex / positive regulation of smooth muscle cell migration / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / response to amine / response to muscle activity / cell-substrate adhesion / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / ECM proteoglycans / detection of mechanical stimulus involved in sensory perception of pain / Integrin cell surface interactions / collagen binding / laminin binding / axon terminus / extracellular matrix organization / positive regulation of smooth muscle cell proliferation / positive regulation of cell adhesion / positive regulation of translation / animal organ morphogenesis / cell-matrix adhesion / integrin-mediated signaling pathway / cellular response to estradiol stimulus / cellular response to mechanical stimulus / female pregnancy / cell-cell adhesion / integrin binding / blood coagulation / 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, 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 Ig-like domain 3 / von Willebrand factor, type A domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Integrin alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.153 Å
AuthorsBrown, K.L. / Banerjee, S.
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 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 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
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Integrin alpha-2
A: Integrin alpha-2
B: Integrin alpha-2
D: Integrin alpha-2
E: Integrin alpha-2
F: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,80521
Polymers129,8856
Non-polymers92115
Water6,557364
1
C: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6882
Polymers21,6471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9616
Polymers21,6471
Non-polymers3135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7233
Polymers21,6471
Non-polymers762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0076
Polymers21,6471
Non-polymers3605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6882
Polymers21,6471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7402
Polymers21,6471
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.066, 144.066, 130.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11E-159-

ASN

21A-302-

CL

31F-301-

GOL

41F-441-

HOH

51F-443-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 7:20 or (resid 21 and (name...
21(chain B and (resseq 7:20 or (resid 21 and (name...
31(chain C and (resseq 7:20 or (resid 21 and (name...
41(chain D and (resseq 7:20 or (resid 21 and (name...
51(chain E and (resseq 7:20 or (resid 21 and (name...
61(chain F and (resseq 7:20 or (resid 21 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUILEILE(chain A and (resseq 7:20 or (resid 21 and (name...AB7 - 203 - 16
12TYRTYRTYRTYR(chain A and (resseq 7:20 or (resid 21 and (name...AB2117
13SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
14SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
15SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
16SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
17SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
18SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
19SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
110SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
111SERSERGLYGLY(chain A and (resseq 7:20 or (resid 21 and (name...AB6 - 2012 - 197
21LEULEUILEILE(chain B and (resseq 7:20 or (resid 21 and (name...BC7 - 203 - 16
22TYRTYRTYRTYR(chain B and (resseq 7:20 or (resid 21 and (name...BC2117
23SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
24SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
25SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
26SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
27SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
28SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
29SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
210SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
211SERSERGLYGLY(chain B and (resseq 7:20 or (resid 21 and (name...BC6 - 2012 - 197
31LEULEUILEILE(chain C and (resseq 7:20 or (resid 21 and (name...CA7 - 203 - 16
32TYRTYRTYRTYR(chain C and (resseq 7:20 or (resid 21 and (name...CA2117
33PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
34PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
35PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
36PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
37PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
38PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
39PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
310PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
311PROPROGLYGLY(chain C and (resseq 7:20 or (resid 21 and (name...CA5 - 2011 - 197
41LEULEUILEILE(chain D and (resseq 7:20 or (resid 21 and (name...DD7 - 203 - 16
42TYRTYRTYRTYR(chain D and (resseq 7:20 or (resid 21 and (name...DD2117
43PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
44PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
45PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
46PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
47PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
48PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
49PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
410PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
411PROPROGLYGLY(chain D and (resseq 7:20 or (resid 21 and (name...DD5 - 2011 - 197
51LEULEUILEILE(chain E and (resseq 7:20 or (resid 21 and (name...EE7 - 203 - 16
52TYRTYRTYRTYR(chain E and (resseq 7:20 or (resid 21 and (name...EE2117
53SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
54SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
55SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
56SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
57SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
58SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
59SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
510SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
511SERSERGLYGLY(chain E and (resseq 7:20 or (resid 21 and (name...EE6 - 2012 - 197
61LEULEUILEILE(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 203 - 16
62TYRTYRTYRTYR(chain F and (resseq 7:20 or (resid 21 and (name...FF2117
63LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
64LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
65LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
66LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
67LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
68LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
69LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
610LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197
611LEULEUGLYGLY(chain F and (resseq 7:20 or (resid 21 and (name...FF7 - 2013 - 197

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Components

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Protein , 1 types, 6 molecules CABDEF

#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: 21647.459 Da / Num. of mol.: 6 / Fragment: VWFA domain residues 170-366
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

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Non-polymers , 6 types, 379 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, HEPES, calcium 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: 2.15→150 Å / Num. obs: 74386 / % possible obs: 99.3 % / Redundancy: 8 % / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.153→101.87 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 1999 2.71 %
Rwork0.2341 --
obs0.2354 73728 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.153→101.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9094 0 43 364 9501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019264
X-RAY DIFFRACTIONf_angle_d1.25112540
X-RAY DIFFRACTIONf_dihedral_angle_d14.0465528
X-RAY DIFFRACTIONf_chiral_restr0.0681447
X-RAY DIFFRACTIONf_plane_restr0.0071614
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4729X-RAY DIFFRACTION11.26TORSIONAL
12B4729X-RAY DIFFRACTION11.26TORSIONAL
13C4729X-RAY DIFFRACTION11.26TORSIONAL
14D4729X-RAY DIFFRACTION11.26TORSIONAL
15E4729X-RAY DIFFRACTION11.26TORSIONAL
16F4729X-RAY DIFFRACTION11.26TORSIONAL

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