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- PDB-3vi3: Crystal structure of alpha5beta1 integrin headpiece (ligand-free form) -

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Basic information

Entry
Database: PDB / ID: 3vi3
TitleCrystal structure of alpha5beta1 integrin headpiece (ligand-free form)
Components
  • (SG/19 Fab fragment ...) x 2
  • Integrin alpha-5Integrin alpha 5
  • Integrin beta-1
KeywordsCELL ADHESION/IMMUNE SYSTEM / beta propeller fold / Rossmann fold / beta sandwich / 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 / formation of radial glial scaffolds / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / 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 / cell projection organization / Platelet Adhesion to exposed collagen / 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 / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / positive regulation of cell-substrate adhesion / myoblast differentiation / integrin complex / dendrite morphogenesis / Basigin interactions / muscle organ development / Molecules associated with elastic fibres / sarcomere organization / lamellipodium assembly / cell adhesion mediated by integrin / negative regulation of Rho protein signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / MET activates PTK2 signaling / maintenance of blood-brain barrier / Syndecan interactions / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / positive regulation of neuroblast proliferation / epidermal growth factor receptor binding / 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 / negative regulation of anoikis / negative regulation of neuron differentiation / ECM proteoglycans / intercalated disc / RAC3 GTPase cycle / RAC2 GTPase cycle / laminin binding / Integrin cell surface interactions / cellular defense response / coreceptor activity / phagocytosis / ruffle
Similarity search - Function
Integrin domains. Chain A, domain 2 / 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 domains. Chain A, domain 2 / 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. / Immunoglobulins / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNagae, M. / Nogi, T. / Takagi, J.
CitationJournal: J.Cell Biol. / Year: 2012
Title: Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor
Authors: Nagae, M. / Re, S. / Mihara, E. / Nogi, T. / Sugita, Y. / Takagi, J.
History
DepositionSep 21, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-5
B: Integrin beta-1
C: Integrin alpha-5
D: Integrin beta-1
L: SG/19 Fab fragment (Light chain)
H: SG/19 Fab fragment (Heavy chain)
E: SG/19 Fab fragment (Light chain)
F: SG/19 Fab fragment (Heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,84737
Polymers332,8908
Non-polymers5,95829
Water0
1
A: Integrin alpha-5
B: Integrin beta-1
E: SG/19 Fab fragment (Light chain)
F: SG/19 Fab fragment (Heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,53419
Polymers166,4454
Non-polymers3,08915
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Integrin alpha-5
D: Integrin beta-1
L: SG/19 Fab fragment (Light chain)
H: SG/19 Fab fragment (Heavy chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,31318
Polymers166,4454
Non-polymers2,86814
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.956, 102.805, 125.079
Angle α, β, γ (deg.)76.10, 70.19, 71.28
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 68188.523 Da / Num. of mol.: 2 / Fragment: UNP residues 42-664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FNRA, ITGA5 / Cell (production host): CHO-lec3.2.8.1 cell / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08648
#2: Protein Integrin beta-1 / Fibronectin receptor subunit beta / VLA-4 subunit beta


Mass: 50562.000 Da / Num. of mol.: 2 / Fragment: UNP residues 21-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FNRB, ITGB1, MDF2, MSK12 / Cell (production host): CHO-lec3.2.8.1 cell / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05556

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Antibody , 2 types, 4 molecules LEHF

#3: Antibody SG/19 Fab fragment (Light chain)


Mass: 24216.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Mus musculus (house mouse)
#4: Antibody SG/19 Fab fragment (Heavy chain)


Mass: 23478.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Mus musculus (house mouse)

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Sugars , 3 types, 15 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#6: 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.: 2
Source method: isolated from a genetically manipulated source
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
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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 , 2 types, 14 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Sequence details1. THE SEQUENCE CONFLICTS OF ENTITY 2 (INTEGRIN BETA-1) ARE BASED ON REFERENCE 1 OF DATABASE ...1. THE SEQUENCE CONFLICTS OF ENTITY 2 (INTEGRIN BETA-1) ARE BASED ON REFERENCE 1 OF DATABASE UNIPROTKB/SWISS-PROT P05556 (ITB1_HUMAN). 2. THE SEQUENCE OF SG/19 LIGHT CHAIN HAS BEEN DEPOSITED TO EMBL WITH ACCESSION NUMBER HE578878, AND SG/19 HEAVY CHAIN SG/19 HAS BEEN DEPOSITED TO EMBL WITH ACCESSION NUMBER HE578877.

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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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris (pH6.5), 20%(w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2010 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→116.39 Å / Num. all: 91525 / Num. obs: 90446 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rsym value: 0.061 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.462 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→100 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.896 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26683 4480 5 %RANDOM
Rwork0.20696 ---
obs0.21001 85066 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.736 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-0.99 Å25.47 Å2
2---0.18 Å21.39 Å2
3----4.81 Å2
Refinement stepCycle: LAST / Resolution: 2.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22435 0 368 0 22803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223435
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.97831789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64952911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0324.458996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.426153703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.54315112
X-RAY DIFFRACTIONr_chiral_restr0.0860.23550
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 316 -
Rwork0.329 6256 -
obs--98.38 %

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