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- PDB-6jy3: Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully ... -

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Basic information

Entry
Database: PDB / ID: 6jy3
TitleMonomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
Components(Cytochrome c oxidase subunit ...) x 13
KeywordsOXIDOREDUCTASE / Monomer / Fully Oxidized
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation ...Complex IV assembly / TP53 Regulates Metabolic Genes / respiratory chain complex IV assembly / Cytoprotection by HMOX1 / mitochondrial respirasome assembly / Respiratory electron transport / respiratory chain complex IV / respiratory chain complex / cytochrome-c oxidase / oxidative phosphorylation / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / Mitochondrial protein degradation / ATP synthesis coupled electron transport / enzyme regulator activity / aerobic respiration / central nervous system development / respiratory electron transport chain / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G ...Cytochrome c oxidase, subunit VIb / Cytochrome C Oxidase; Chain D / Cytochrome c oxidase subunit IV / Cytochrome C Oxidase; Chain K / Cytochrome C Oxidase, chain K / Cytochrome c oxidase, subunit 8 / Cytochrome c oxidase, subunit VIIa / Cytochrome C Oxidase; Chain I / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome C Oxidase; Chain G / Cytochrome c oxidase, subunit VIa / Cytochrome C Oxidase; Chain M / Cytochrome C Oxidase; Chain L / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit III, four-helix bundle / Cytochrome C Oxidase; Chain J / Helix Hairpins - #90 / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Helix Hairpins - #70 / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Few Secondary Structures / Irregular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Helix Hairpins / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CARDIOLIPIN / CHOLIC ACID / Chem-CQX / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / PEROXIDE ION / Chem-PGV / Cytochrome c oxidase subunit 1 ...CARDIOLIPIN / CHOLIC ACID / Chem-CQX / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / Chem-PEK / PEROXIDE ION / Chem-PGV / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 4 isoform 1, mitochondrial / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase subunit 8B, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsShinzawa-Itoh, K. / Muramoto, K.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceKAKENHI Grant 117048028 Japan
Japan Society for the Promotion of ScienceKAKENHI Grant 22570122 Japan
Japan Society for the Promotion of ScienceKAKENHI Grant 17H03646 Japan
Japan Society for the Promotion of ScienceKAKENHI Grant 22370060 Japan
Japan Society for the Promotion of ScienceKAKENHI Grant 15K07029 Japan
Japan Society for the Promotion of ScienceKAKENHI Grant 18K06162 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Monomeric structure of an active form of bovine cytochromecoxidase.
Authors: Shinzawa-Itoh, K. / Sugimura, T. / Misaki, T. / Tadehara, Y. / Yamamoto, S. / Hanada, M. / Yano, N. / Nakagawa, T. / Uene, S. / Yamada, T. / Aoyama, H. / Yamashita, E. / Tsukihara, T. / ...Authors: Shinzawa-Itoh, K. / Sugimura, T. / Misaki, T. / Tadehara, Y. / Yamamoto, S. / Hanada, M. / Yano, N. / Nakagawa, T. / Uene, S. / Yamada, T. / Aoyama, H. / Yamashita, E. / Tsukihara, T. / Yoshikawa, S. / Muramoto, K.
History
DepositionApr 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 3
D: Cytochrome c oxidase subunit 4 isoform 1
E: Cytochrome c oxidase subunit 5A
F: Cytochrome c oxidase subunit 5B
G: Cytochrome c oxidase subunit 6A2, mitochondrial
H: Cytochrome c oxidase subunit 6B1
I: Cytochrome c oxidase subunit 6C
J: Cytochrome c oxidase subunit 7A1
K: Cytochrome c oxidase subunit 7B
L: Cytochrome c oxidase subunit 7C, mitochondrial
M: Cytochrome c oxidase subunit 8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,03237
Polymers204,98613
Non-polymers12,04724
Water11,926662
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.529, 152.131, 174.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Cytochrome c oxidase subunit ... , 13 types, 13 molecules ABCDEFGHIJKLM

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 57093.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00396, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 26068.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P68530
#3: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29957.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00415
#4: Protein Cytochrome c oxidase subunit 4 isoform 1 / Cytochrome c oxidase polypeptide IV


Mass: 17179.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00423
#5: Protein Cytochrome c oxidase subunit 5A / Cytochrome c oxidase polypeptide Va


Mass: 12453.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00426
#6: Protein Cytochrome c oxidase subunit 5B / Cytochrome c oxidase polypeptide VIa


Mass: 10684.038 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00428
#7: Protein Cytochrome c oxidase subunit 6A2, mitochondrial / Cytochrome c oxidase polypeptide VIa-heart / COXVIAH / Cytochrome c oxidase polypeptide VIb


Mass: 9549.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07471
#8: Protein Cytochrome c oxidase subunit 6B1 / Cytochrome c oxidase polypeptide VII


Mass: 10039.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00429
#9: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc / Cytochrome c oxidase subunit STA


Mass: 8494.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P04038
#10: Protein Cytochrome c oxidase subunit 7A1 / Cytochrome c oxidase subunit VIIIc / VIIIC


Mass: 6682.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07470
#11: Protein Cytochrome c oxidase subunit 7B / Cytochrome c oxidase polypeptide VIIb


Mass: 6365.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13183
#12: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIIA


Mass: 5449.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00430
#13: Protein/peptide Cytochrome c oxidase subunit 8B / Cytochrome c oxidase polypeptide VIII-heart


Mass: 4967.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P10175

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Non-polymers , 13 types, 686 molecules

#14: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#15: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#17: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#18: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#19: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#20: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#21: Chemical
ChemComp-CQX / (2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl)oxane-3,4,5-triol / 3-Oxatridecyl-alpha-D-mannopyranoside


Mass: 364.474 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H36O7 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#23: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-PEK / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE / PHOSPHATIDYLETHANOLAMINE / 2-ARACHIDONOYL-1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE


Mass: 768.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H78NO8P / Comment: phospholipid*YM
#25: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#26: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.84 Å3/Da / Density % sol: 74.6 %
Crystal growTemperature: 277 K / Method: batch mode / Details: sodium phosphate, PEG 4000, DM

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Data collection

DiffractionMean temperature: 50 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→200 Å / Num. obs: 361138 / % possible obs: 99.3 % / Redundancy: 7.4 % / Rpim(I) all: 0.031 / Net I/σ(I): 29.3
Reflection shellResolution: 1.8→1.82 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 12029 / CC1/2: 0.765 / Rpim(I) all: 0.459

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B1A

5b1a


Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.565 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.079 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19162 16494 5 %RANDOM
Rwork0.15125 ---
obs0.15326 316483 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.877 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0 Å2
2--3.49 Å2-0 Å2
3----4.35 Å2
Refinement stepCycle: 1 / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13851 0 729 662 15242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02315060
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214359
X-RAY DIFFRACTIONr_angle_refined_deg2.039220367
X-RAY DIFFRACTIONr_angle_other_deg1.0023.00733103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87751716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29222.95600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15152267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8061562
X-RAY DIFFRACTIONr_chiral_restr0.1190.22190
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02116106
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023523
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_it6.6653.7376903
X-RAY DIFFRACTIONr_mcbond_other6.6553.7376902
X-RAY DIFFRACTIONr_mcangle_it7.2335.6058606
X-RAY DIFFRACTIONr_mcangle_other7.2335.6058607
X-RAY DIFFRACTIONr_scbond_it9.664.348157
X-RAY DIFFRACTIONr_scbond_other9.664.348157
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1516.30911762
X-RAY DIFFRACTIONr_long_range_B_refined9.14832.0917878
X-RAY DIFFRACTIONr_long_range_B_other9.0931.95117632
X-RAY DIFFRACTIONr_rigid_bond_restr6.906329419
X-RAY DIFFRACTIONr_sphericity_free48.5035170
X-RAY DIFFRACTIONr_sphericity_bonded25.134529434
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 1141 -
Rwork0.223 23405 -
obs--99.68 %
Refinement TLS params.Method: refined / Origin x: 39.8831 Å / Origin y: 60.8675 Å / Origin z: 5.4681 Å
111213212223313233
T0 Å20.0005 Å20.0004 Å2-0.0169 Å2-0.0013 Å2--0.059 Å2
L0.0313 °20.0003 °20.0016 °2-0 °20.0001 °2--0.0253 °2
S-0.0003 Å °-0.0041 Å °0.0078 Å °-0 Å °-0 Å °-0.0003 Å °0.0003 Å °-0.0019 Å °0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 514
2X-RAY DIFFRACTION1A601 - 607
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION1C301
5X-RAY DIFFRACTION1B1 - 227
6X-RAY DIFFRACTION1B302 - 304
7X-RAY DIFFRACTION1C4 - 257
8X-RAY DIFFRACTION1A608
9X-RAY DIFFRACTION1C302 - 307
10X-RAY DIFFRACTION1G101
11X-RAY DIFFRACTION1D11 - 146
12X-RAY DIFFRACTION1E7 - 108
13X-RAY DIFFRACTION1F3 - 93
14X-RAY DIFFRACTION1F101
15X-RAY DIFFRACTION1G12 - 83
16X-RAY DIFFRACTION1H11 - 85
17X-RAY DIFFRACTION1I3 - 72
18X-RAY DIFFRACTION1J1 - 55
19X-RAY DIFFRACTION1K6 - 54
20X-RAY DIFFRACTION1A609
21X-RAY DIFFRACTION1L3 - 46
22X-RAY DIFFRACTION1A610
23X-RAY DIFFRACTION1M1 - 40
24X-RAY DIFFRACTION1A611
25X-RAY DIFFRACTION1A702 - 903
26X-RAY DIFFRACTION1B402 - 524
27X-RAY DIFFRACTION1C401 - 477
28X-RAY DIFFRACTION1D201 - 241
29X-RAY DIFFRACTION1E203 - 231
30X-RAY DIFFRACTION1F201 - 243
31X-RAY DIFFRACTION1G202 - 236
32X-RAY DIFFRACTION1H101 - 140
33X-RAY DIFFRACTION1I102 - 116
34X-RAY DIFFRACTION1J101 - 107
35X-RAY DIFFRACTION1K101 - 111
36X-RAY DIFFRACTION1L102 - 113
37X-RAY DIFFRACTION1M102 - 109

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  • 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

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