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- PDB-1dzi: integrin alpha2 I domain / collagen complex -

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Basic information

Entry
Database: PDB / ID: 1dzi
Titleintegrin alpha2 I domain / collagen complex
Components
  • COLLAGEN
  • INTEGRIN
KeywordsINTEGRIN / COLLAGEN
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 / skin morphogenesis / CHL1 interactions / 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 / heparan sulfate proteoglycan binding / mesodermal cell differentiation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / integrin complex / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / positive regulation of smooth muscle cell migration / response to muscle activity / 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
: / Integrin alpha-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEmsley, j. / Knight, G. / Farndale, R. / Barnes, M. / Liddington, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural Basis of Collagen Recognition by Integrin Alpha2Beta1
Authors: Emsley, J. / Knight, G. / Farndale, R. / Barnes, M. / Liddington, R.
History
DepositionMar 1, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Advisory / Derived calculations / Source and taxonomy
Category: database_PDB_caveat / pdbx_entity_src_syn ...database_PDB_caveat / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._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
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTEGRIN
B: COLLAGEN
C: COLLAGEN
D: COLLAGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4575
Polymers26,3984
Non-polymers591
Water7,278404
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-34.6 kcal/mol
Surface area14780 Å2
MethodPQS
Unit cell
Length a, b, c (Å)41.994, 48.377, 114.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTEGRIN


Mass: 20359.053 Da / Num. of mol.: 1 / Fragment: ALPHA2 I DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17301
#2: Protein/peptide COLLAGEN


Mass: 2013.130 Da / Num. of mol.: 3 / Fragment: TRIMERIC GPOGPOGFOGERGPOGPOGPO 21MERIC PEPTIDE / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHAIN A: C-TERMINAL ALA IS A SER IN ITA2_HUMAN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 MTris1drop
20.15 M1dropNaCl
32 mM1dropMgCl2or MnCl2
410 mMacetate1drop
525 mMsodium cacodylate1reservoir
620 %glycerol1reservoir
720-30 %PEG5000 MMK1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 14483 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.9

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: THE RESIDUES B1-3,C1-3,D1-3 ARE IN POOR DENSITY
RfactorNum. reflection% reflectionSelection details
Rwork0.1999 ---
obs0.1999 11809 83.2 %-
Rfree-595 5 %0.2729
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 1 404 2266
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.203 / Rfactor Rfree: 0.2729 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS

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