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- PDB-1v7p: Structure of EMS16-alpha2-I domain complex -

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Basic information

Entry
Database: PDB / ID: 1v7p
TitleStructure of EMS16-alpha2-I domain complex
Components
  • EMS16 A chain
  • EMS16 B chain
  • Integrin alpha-2
KeywordsTOXIN/CELL ADHESION / SNAKE VENOM / C-TYPE LECTIN / ANTAGONIST / INTEGRIN / CELL ADHESION / GLYCOPROTEIN / TOXIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


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 / hypotonic response / response to L-ascorbic acid / skin morphogenesis ...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 / hypotonic response / response to L-ascorbic acid / skin morphogenesis / CHL1 interactions / Laminin interactions / basal part of cell / positive regulation of smooth muscle contraction / positive regulation of phagocytosis, engulfment / collagen-activated signaling pathway / mammary gland development / Platelet Adhesion to exposed collagen / hepatocyte differentiation / mesodermal cell differentiation / focal adhesion assembly / heparan sulfate proteoglycan binding / response to muscle activity / integrin complex / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / cell-substrate adhesion / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / response to amine / positive regulation of cell adhesion / ECM proteoglycans / positive regulation of collagen biosynthetic process / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / axon terminus / laminin binding / collagen binding / cell-matrix adhesion / cellular response to estradiol stimulus / positive regulation of translation / integrin-mediated signaling pathway / female pregnancy / 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 / signaling receptor activity / amyloid-beta binding / toxin activity / cell adhesion / response to hypoxia / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / von Willebrand factor, type A domain / : / 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 Ig-like domain 3 / von Willebrand factor, type A domain / : / 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 / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Integrin alpha-2 / Snaclec EMS16 subunit beta / Snaclec EMS16 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Echis multisquamatus (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHorii, K. / Okuda, D. / Morita, T. / Mizuno, H.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of EMS16 in complex with the integrin alpha2-I domain
Authors: Horii, K. / Okuda, D. / Morita, T. / Mizuno, H.
#1: Journal: Biochemistry / Year: 2003
Title: Structural Charcterization of EMS16, an Antagonist of Collagen Receptor (GPIa/IIa) from the Venom of Echis multisquamatus
Authors: Horii, K. / Okuda, D. / Morita, T. / Mizuno, H.
#2: Journal: 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.
#3: Journal: CELL(CAMBRIDGE,MASS.) / Year: 2000
Title: Structural basis of collagen recognition by integrin alpha2beta1
Authors: Emsley, J. / Knight, C.G. / Farndale, R.W. / Barnes, M.J. / Liddington, R.C.
History
DepositionDec 19, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EMS16 A chain
B: EMS16 B chain
C: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2967
Polymers52,8903
Non-polymers4074
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.766, 38.449, 69.524
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1509-

HOH

21C-1528-

HOH

31C-1543-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein EMS16 A chain / EMS16 subunit A


Mass: 15889.537 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-134 / Source method: isolated from a natural source / Source: (natural) Echis multisquamatus (snake) / References: UniProt: Q7T2Q1
#2: Protein EMS16 B chain / EMS16 subunit B


Mass: 15121.384 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-128 / Mutation: G43S / Source method: isolated from a natural source / Source: (natural) Echis multisquamatus (snake) / References: UniProt: Q7T2Q0
#3: Protein Integrin alpha-2 / alpha2-I / Platelet membrane glycoprotein Ia / GPIa / Collagen receptor / VLA-2 alpha chain / CD49b


Mass: 21878.668 Da / Num. of mol.: 1 / Fragment: RESIDUES 138-337 / Mutation: Q138G, P139S, C140S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17301

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Sugars , 1 types, 1 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 466 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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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: 1.88 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG8000, POTASSIUM DIHYDROGEN PHOSPHATE, SODIUM CHLORIDE, MALONIC ACID, MANGANESE CHLORIDE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 33974 / % possible obs: 97 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.209 / % possible all: 84.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1880292.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1693 5 %RANDOM
Rwork0.188 ---
obs-33892 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7106 Å2 / ksol: 0.350776 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1--6.72 Å20 Å2-0.65 Å2
2--11.41 Å20 Å2
3----4.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3669 0 21 463 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 279 5.3 %
Rwork0.217 5028 -
obs--92.7 %

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