[English] 日本語
Yorodumi
- PDB-6giq: Saccharomyces cerevisiae respiratory supercomplex III2IV -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6giq
TitleSaccharomyces cerevisiae respiratory supercomplex III2IV
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • (Cytochrome c oxidase polypeptide ...) x 2
  • (Cytochrome c oxidase subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
  • Unknown Cox subunit
KeywordsELECTRON TRANSPORT / Respiratory chain / supercomplex / bc1 complex / cytochrome c oxidase
Function / homologyCytochrome c oxidase subunit I domain / Cytochrome b-c1 complex subunit 10, fungi / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Va / Cytochrome b / Cytochrome b/b6-like domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site ...Cytochrome c oxidase subunit I domain / Cytochrome b-c1 complex subunit 10, fungi / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Va / Cytochrome b / Cytochrome b/b6-like domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit I, copper-binding site / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c oxidase, subunit Vb, zinc binding site / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome b/b6, C-terminal domain superfamily / Rieske [2Fe-2S] iron-sulphur domain / Di-haem cytochrome, transmembrane / Cytochrome c oxidase, subunit VIIa, fungal / Cytochrome c oxidase subunit VII, budding yeast / Rieske iron-sulphur protein / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit III, 4-helical bundle / Peptidase M16, N-terminal / Cytochrome C oxidase subunit II, transmembrane domain / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome C1 family / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase subunit Vb / Insulinase (Peptidase family M16) / Cytochrome c oxidase subunit III / Rieske [2Fe-2S] domain / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6/petB / Cytochrome b(C-terminal)/b6/petD / Cytochrome c oxidase subunit VII / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase-like, subunit I superfamily / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c-like domain superfamily / Ubiquinol-cytochrome C reductase hinge domain superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome b-c1 complex subunit 7 superfamily / Cupredoxin / Peptidase M16, C-terminal / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c oxidase subunit IV / UcrQ family / Peptidase M16 inactive domain / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome-c reductase complex subunit (QCR10) / Heme-copper oxidase catalytic subunit, copper B binding region signature. / CO II and nitrous oxide reductase dinuclear copper centers signature. / Insulinase family, zinc-binding region signature. / Cytochrome c oxidase subunit VIa signature. / Cytochrome C oxidase subunit II, transmembrane domain / Heme-copper oxidase subunit III family profile. / Cytochrome oxidase subunit I profile. / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b/b6 N-terminal region profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome c family profile. / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Ubiquinol cytochrome reductase transmembrane region / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit VII / Ubiquinol-cytochrome C reductase hinge protein / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase subunit VIIc / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome c1 / Cytochrome c oxidase, subunit Vb / Cytochrome oxidase c subunit VIb / Copper centre Cu(A) / Cytochrome c oxidase subunit III-like
Function and homology information
Specimen sourceSaccharomyces cerevisiae W303 (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.23 Å resolution
AuthorsRathore, S. / Berndtsson, J. / Conrad, J. / Ott, M.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 15, 2018 / Release: Jan 2, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 2, 2019Structure modelrepositoryInitial release
1.1Jan 9, 2019Structure modelData collection / Database referencescitation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod
1.2Jan 16, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0004
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 6
G: Cytochrome b-c1 complex subunit 7
H: Cytochrome b-c1 complex subunit 8
I: Cytochrome b-c1 complex subunit 9
L: Cytochrome b-c1 complex subunit 1, mitochondrial
M: Cytochrome b-c1 complex subunit 2, mitochondrial
N: Cytochrome b
O: Cytochrome c1, heme protein, mitochondrial
P: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Q: Cytochrome b-c1 complex subunit 6
R: Cytochrome b-c1 complex subunit 7
S: Cytochrome b-c1 complex subunit 8
T: Cytochrome b-c1 complex subunit 9
U: Cytochrome b-c1 complex subunit 10
V: Cytochrome b-c1 complex subunit 10
a: Cytochrome c oxidase subunit 1
b: Cytochrome c oxidase subunit 2
c: Cytochrome c oxidase subunit 3
d: Cytochrome c oxidase subunit 4, mitochondrial
e: Cytochrome c oxidase polypeptide 5A, mitochondrial
f: Cytochrome c oxidase subunit 6, mitochondrial
g: Cytochrome c oxidase subunit 7
h: Cytochrome c oxidase polypeptide VIII, mitochondrial
i: Cytochrome c oxidase subunit 7A
j: Cytochrome c oxidase subunit 6B
k: Cytochrome c oxidase subunit 6A, mitochondrial
m: Unknown Cox subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)736,64058
Polyers721,68332
Non-polymers14,95726
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Other experiment performed that support the state of this assembly is native gel electrophoresis and co-purification combined with determination of enzyme quantity.
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)128830
ΔGint (kcal/M)-1044
Surface area (Å2)224990
MethodPISA

-
Components

-
Cytochrome b-c1 complex subunit ... , 8 types, 16 molecules ALBMEPFQGRHSITUV

#1: Protein/peptide Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 50282.594 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07256
#2: Protein/peptide Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 40528.008 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07257
#5: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 23393.973 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P08067, quinol-cytochrome-c reductase
#6: Protein/peptide Cytochrome b-c1 complex subunit 6 / Complex III subunit 6 / Complex III subunit VI / Cytochrome c1 non-heme 17 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 17 kDa protein


Mass: 17276.074 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00127
#7: Protein/peptide Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / Ubiquinol-cytochrome c reductase c reductase complex 14 kDa protein


Mass: 14583.755 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00128
#8: Protein/peptide Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VII / Ubiquinol-cytochrome c reductase complex 11 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 10987.511 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P08525
#9: Protein/peptide Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7.3 kDa protein / Ubiquinol-cytochrome c reductase complex 7.3 kDa protein


Mass: 7485.334 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P22289
#10: Protein/peptide Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 8.5 kDa protein


Mass: 8602.913 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P37299

-
Protein/peptide , 3 types, 5 molecules CNDOm

#3: Protein/peptide Cytochrome b / / Complex III subunit 3 / Complex III subunit CYTB / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Cytochrome b-c1 complex subunit CYTB / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 43686.590 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00163
#4: Protein/peptide Cytochrome c1, heme protein, mitochondrial / / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


Mass: 34097.523 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07143
#22: Protein/peptide Unknown Cox subunit


Mass: 2656.265 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast)

-
Cytochrome c oxidase subunit ... , 9 types, 9 molecules abcdfgijk

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


Mass: 58832.586 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00401, cytochrome-c oxidase
#12: Protein/peptide Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II


Mass: 28585.055 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00410, cytochrome-c oxidase
#13: Protein/peptide Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III


Mass: 30383.582 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00420, cytochrome-c oxidase
#14: Protein/peptide Cytochrome c oxidase subunit 4, mitochondrial / / Cytochrome c oxidase polypeptide IV


Mass: 17164.557 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04037, cytochrome-c oxidase
#16: Protein/peptide Cytochrome c oxidase subunit 6, mitochondrial / / Cytochrome c oxidase polypeptide VI


Mass: 17366.600 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00427, cytochrome-c oxidase
#17: Protein/peptide Cytochrome c oxidase subunit 7 / / Cytochrome c oxidase polypeptide VII


Mass: 6942.349 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P10174, cytochrome-c oxidase
#19: Protein/peptide Cytochrome c oxidase subunit 7A / / Cytochrome c oxidase polypeptide VIIA


Mass: 6974.226 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P07255, cytochrome-c oxidase
#20: Protein/peptide Cytochrome c oxidase subunit 6B / / Cytochrome c oxidase polypeptide VIb


Mass: 9799.895 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: Q01519, cytochrome-c oxidase
#21: Protein/peptide Cytochrome c oxidase subunit 6A, mitochondrial / / Cytochrome c oxidase polypeptide VIa


Mass: 15046.146 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P32799, cytochrome-c oxidase

-
Cytochrome c oxidase polypeptide ... , 2 types, 2 molecules eh

#15: Protein/peptide Cytochrome c oxidase polypeptide 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 17161.465 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P00424, cytochrome-c oxidase
#18: Protein/peptide Cytochrome c oxidase polypeptide VIII, mitochondrial


Mass: 8921.686 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae W303 (yeast) / References: UniProt: P04039, cytochrome-c oxidase

-
Non-polymers , 13 types, 26 molecules

#23: Chemical ChemComp-6PH / (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate / PHOSPHATIDIC ACID


Mass: 592.785 Da / Num. of mol.: 2 / Formula: C31H61O8P / Phosphatidic acid
#24: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Formula: C34H32FeN4O4 / Heme
#25: Chemical ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 691.959 Da / Num. of mol.: 2 / Formula: C37H74NO8P / Comment: phospholipid *YM
#26: Chemical ChemComp-CN5 / (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate / CARDIOLIPIN


Mass: 634.631 Da / Num. of mol.: 1 / Formula: C26H52O13P2 / Cardiolipin
#27: Chemical ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 2 / Formula: C39H60O4
#28: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 2 / Formula: C29H57O8P / Phosphatidic acid
#29: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#30: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 2 / Formula: C40H80NO8P
#31: Chemical ChemComp-9PE / (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


Mass: 593.773 Da / Num. of mol.: 2 / Formula: C30H60NO8P / Comment: phospholipid *YM
#32: Chemical ChemComp-CN3 / (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate / CARDIOLIPIN


Mass: 834.862 Da / Num. of mol.: 1 / Formula: C36H68O17P2 / Cardiolipin
#33: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Formula: Cu / Copper
#34: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Formula: C49H56FeN4O6 / Heme A
#35: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Formula: Cu2

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Saccharomyces cerevisiae Supercomplex (III2IV)COMPLEX1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,220NATURAL
2Saccharomyces cerevisiae complex IIICOMPLEX1,2,3,4,5,6,7,8,9,101NATURAL
3Saccharomyces cerevisiae complex IVCOMPLEX11,12,13,14,15,16,17,18,19,20,21,221NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganelleOrganism
21580240MitochondriaSaccharomyces cerevisiae W303 (yeast)
32580240MitochondriaSaccharomyces cerevisiae W303 (yeast)
43580240MitochondriaSaccharomyces cerevisiae W303 (yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
9PHENIX1.13model refinement
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 203271 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL / Target criteria: Cross-Correlation coefficient

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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