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- PDB-7jrp: Plant Mitochondrial complex SC III2+IV from Vigna radiata -

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Basic information

Entry
Database: PDB / ID: 7jrp
TitlePlant Mitochondrial complex SC III2+IV from Vigna radiata
Components
  • (Cytochrome b-c1 complex subunit ...) x 5
  • (Cytochrome c oxidase subunit ...) x 5
  • Alpha-MPP
  • COB
  • COX1
  • COX3
  • COX4
  • COX7a
  • COX7c
  • Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
  • QCR10
  • cytochrome c1-2, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / mitochondria / respiration / bioenergetics / plants
Function / homology
Function and homology information


mitochondrial processing peptidase / membrane protein complex / respiratory chain complex IV / mitochondrial envelope / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...mitochondrial processing peptidase / membrane protein complex / respiratory chain complex IV / mitochondrial envelope / respiratory chain complex III / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / catalytic complex / ATP synthesis coupled electron transport / enzyme regulator activity / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / copper ion binding / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
Similarity search - Function
Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa ...Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / 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 VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb / 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 b-c1 complex, subunit 6 / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c/quinol oxidase subunit II / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / LYSINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome b-c1 complex subunit Rieske, mitochondrial ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / LYSINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein LOC106757297 / Complex III subunit 9 / Uncharacterized protein LOC106759053 / mitochondrial processing peptidase / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 5b-2, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 6a, mitochondrial / Cytochrome c oxidase subunit 5C / Uncharacterized protein LOC106772338 / Complex III subunit II / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 6b-1 / Cytochrome c1-2, heme protein, mitochondrial
Similarity search - Component
Biological speciesVigna radiata var. radiata (mung bean)
Vigna radiata (mung bean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMaldonado, M. / Letts, J.A.
CitationJournal: Elife / Year: 2021
Title: Atomic structures of respiratory complex III, complex IV, and supercomplex III-IV from vascular plants.
Authors: Maria Maldonado / Fei Guo / James A Letts /
Abstract: Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes ...Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII, CIV, and SC III+IV from determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII revealed long-range, coordinated movements across the complex, as well as the motion of CIII's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: 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 / em_3d_fitting_list / em_admin / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
A: Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
B: Alpha-MPP
C: COB
D: cytochrome c1-2, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6
J: cytochrome b-c1 complex subunit 9
K: QCR10
M: Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1
N: Alpha-MPP
O: COB
P: cytochrome c1-2, heme protein, mitochondrial
Q: Cytochrome b-c1 complex subunit Rieske, mitochondrial
R: Cytochrome b-c1 complex subunit 7
S: cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 6
V: cytochrome b-c1 complex subunit 9
W: QCR10
a: COX1
b: Cytochrome c oxidase subunit 2
c: COX3
d: COX4
e: cytochrome c oxidase subunit 5b-2, mitochondrial
f: cytochrome c oxidase subunit 6a, mitochondrial
g: cytochrome c oxidase subunit 6b-1
h: Cytochrome c oxidase subunit 5C
i: COX7a
j: COX7c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)781,55188
Polymers736,76330
Non-polymers44,78858
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 10 types, 15 molecules AMBNCODPKWacdij

#1: Protein Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 / MPP-beta


Mass: 58711.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TWG4
#2: Protein Alpha-MPP / Inactive zinc metalloprotease alpha / Mitochondrial-processing peptidase subunit alpha


Mass: 54537.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3VF71
#3: Protein COB


Mass: 44353.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#4: Protein cytochrome c1-2, heme protein, mitochondrial


Mass: 33556.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3W199
#10: Protein QCR10


Mass: 8948.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#11: Protein COX1


Mass: 57960.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#13: Protein COX3


Mass: 29967.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#14: Protein COX4


Mass: 8811.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TNX9
#19: Protein COX7a


Mass: 7622.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TUX2
#20: Protein COX7c


Mass: 10505.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3V7C2

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Cytochrome b-c1 complex subunit ... , 5 types, 10 molecules EQFRGSHTJV

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 30051.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean)
References: UniProt: A0A1S3TB49, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7


Mass: 14392.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3U9J1
#7: Protein cytochrome b-c1 complex subunit 8


Mass: 8349.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3U9S5
#8: Protein Cytochrome b-c1 complex subunit 6


Mass: 8117.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3VHC0
#9: Protein cytochrome b-c1 complex subunit 9


Mass: 8203.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TQD2

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Cytochrome c oxidase subunit ... , 5 types, 5 molecules befgh

#12: Protein Cytochrome c oxidase subunit 2


Mass: 28391.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3TZB2
#15: Protein cytochrome c oxidase subunit 5b-2, mitochondrial


Mass: 16694.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3U1E4
#16: Protein cytochrome c oxidase subunit 6a, mitochondrial


Mass: 11225.671 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3UMA0
#17: Protein cytochrome c oxidase subunit 6b-1


Mass: 20018.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3VV60
#18: Protein Cytochrome c oxidase subunit 5C


Mass: 7120.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata var. radiata (mung bean) / References: UniProt: A0A1S3V319

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Non-polymers , 11 types, 58 molecules

#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#22: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#23: 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.: 9 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#24: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#25: Chemical...
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#27: Chemical ChemComp-HEA / HEME-A


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


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#30: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#31: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mitochondrial Respiratory Complex III2 / Type: COMPLEX / Entity ID: #1-#20 / Source: NATURAL
Molecular weightValue: 0.485 MDa / Experimental value: NO
Source (natural)Organism: Vigna radiata (mung bean) / Organelle: mitochondria / Tissue: hypocotyl
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2150 mMsodium chlorideNaCl1
31 mMEDTA1
40.2 %digitonin1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 60010 X / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 86.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9816
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 150000000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29348 / Symmetry type: POINT
Atomic model buildingB value: 67 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16Q9E

6q9e

16Q9E1PDBexperimental model
26HU9

6hu9

16HU92PDBexperimental model

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