[English] 日本語
Yorodumi
- PDB-4wk2: Metal Ion and Ligand Binding of Integrin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wk2
TitleMetal Ion and Ligand Binding of Integrin
Components
  • GLY-ARG-GLY-ASP-SER-PRO
  • Integrin alpha-5Integrin alpha 5
  • Integrin beta-1
KeywordsCELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-FIBRONECTIN RECEPTOR / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / formation of radial glial scaffolds / Other semaphorin interactions / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / alphav-beta3 integrin-vitronectin complex / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / RUNX2 regulates genes involved in cell migration / germ cell migration / MET interacts with TNS proteins / leukocyte tethering or rolling / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / cell projection organization / vascular endothelial growth factor receptor 2 binding / myoblast fusion / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / platelet-derived growth factor receptor binding / axon extension / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / wound healing, spreading of epidermal cells / myoblast differentiation / heterotypic cell-cell adhesion / regulation of spontaneous synaptic transmission / integrin complex / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / lamellipodium assembly / muscle organ development / sarcomere organization / negative regulation of Rho protein signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cell adhesion mediated by integrin / MET activates PTK2 signaling / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / epidermal growth factor receptor binding / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / positive regulation of wound healing / cell-substrate adhesion / positive regulation of sprouting angiogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / cellular response to low-density lipoprotein particle stimulus / fibronectin binding / neuroblast proliferation / RHOG GTPase cycle / intercalated disc / negative regulation of anoikis / negative regulation of neuron differentiation / ECM proteoglycans / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / laminin binding / cellular defense response / coreceptor activity / phagocytosis / ruffle
Similarity search - Function
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / 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 domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXia, W. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Metal ion and ligand binding of integrin alpha 5 beta 1.
Authors: Xia, W. / Springer, T.A.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 2.0Nov 22, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin alpha-5
B: Integrin beta-1
C: GLY-ARG-GLY-ASP-SER-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,03920
Polymers98,2083
Non-polymers4,83117
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-13 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.980, 118.390, 170.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Integrin alpha-5 / Integrin alpha 5 / CD49 antigen-like family member E / Fibronectin receptor subunit alpha / Integrin alpha-F / VLA-5


Mass: 48116.863 Da / Num. of mol.: 1 / Fragment: UNP residues 42-493 / Mutation: I451V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA5, FNRA / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P08648
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / Glycoprotein IIa / GPIIA / VLA-4 subunit beta


Mass: 49502.852 Da / Num. of mol.: 1 / Fragment: UNP residues 21-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1, FNRB, MDF2, MSK12 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P05556

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide GLY-ARG-GLY-ASP-SER-PRO


Mass: 588.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Sugars , 4 types, 10 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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

-
Non-polymers , 3 types, 171 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1 M HEPES 7.2, 16% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→42.57 Å / Num. obs: 42741 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 67.15 Å2 / Net I/σ(I): 7.46

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.57 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2536 1997 4.68 %
Rwork0.2103 40711 -
obs0.2123 42708 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 347.21 Å2 / Biso mean: 99.4632 Å2 / Biso min: 39.15 Å2
Refinement stepCycle: final / Resolution: 2.5→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6739 0 591 164 7494
Biso mean--131.79 74.22 -
Num. residues----881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067278
X-RAY DIFFRACTIONf_angle_d0.7869842
X-RAY DIFFRACTIONf_chiral_restr0.0311133
X-RAY DIFFRACTIONf_plane_restr0.0021264
X-RAY DIFFRACTIONf_dihedral_angle_d12.8852660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56260.45471430.40722917306099
2.5626-2.63190.41191430.39229063049100
2.6319-2.70930.35151400.34852886302699
2.7093-2.79680.38231430.32392914305799
2.7968-2.89670.30111430.30962907305099
2.8967-3.01260.30991430.295729093052100
3.0126-3.14970.311420.2752908305099
3.1497-3.31570.31451420.25712896303899
3.3157-3.52340.26251420.22452884302697
3.5234-3.79520.2661400.20622868300896
3.7952-4.17690.22121390.17152833297296
4.1769-4.78060.20271420.14742904304697
4.7806-6.02030.18831450.16812939308497
6.0203-42.57870.24181500.18463040319096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9615-0.94860.75764.82922.13023.3545-0.34790.0102-0.60730.07890.55161.31850.252-0.5499-0.1720.5454-0.05430.33850.66190.10751.1226-6.1433-18.4387-25.5488
24.1148-0.00180.25611.1725-0.45761.7615-0.1337-0.3909-0.13560.69670.20780.9289-0.2135-0.21950.14790.74760.16790.4420.61120.10870.8581-5.7114-1.3724-14.4074
32.75650.2723-0.89352.9319-0.30382.8516-0.2166-0.3719-0.41480.48540.0444-0.12430.1140.28570.20730.48150.11160.13060.54580.06410.551514.6486-8.9492-19.5528
43.86140.18670.07664.9554-1.51614.3871-0.24770.1164-0.761-0.18230.24490.57580.4801-0.1831-0.03260.5186-0.03710.21890.5214-0.0130.99991.7715-21.7997-33.9984
51.55481.45360.91115.14992.08061.00690.60450.0712-0.88970.4958-0.0369-0.89870.06490.609-0.60511.69710.007-0.01591.0534-0.43171.692421.2411-35.0828-80.5156
62.60311.2095-1.12964.25261.58114.9364-0.29420.4571-0.3293-1.02270.3153-0.081-0.1303-0.0329-0.11510.6324-0.0806-0.02160.53060.05380.533823.14514.1851-67.5089
73.021-0.0323-1.25553.1796-0.77693.39840.16360.01330.4960.24490.07710.0596-0.56950.0865-0.24160.3952-0.06140.06980.3914-0.04580.542717.334114.8675-39.7983
82.10231.58781.57317.28864.67636.1330.33520.1255-0.67030.0280.0329-0.81770.81940.1823-0.3470.7404-0.01220.04010.5320.02420.731325.1362-3.9868-63.1026
93.0522-1.55082.88482.9889-2.6143.3512-0.23620.35592.20450.4329-0.1188-1.6825-1.31291.65410.19521.2456-0.3161-0.12911.1053-0.2341.539723.541713.7807-22.0937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 116 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 350 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 351 through 452 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 65 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 132 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 133 through 346 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 347 through 444 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 5000 through 5005 )C0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more