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- PDB-6hu9: III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae -

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Entry
Database: PDB / ID: 6hu9
TitleIII2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • (Cytochrome c oxidase polypeptide ...) x 2
  • (Cytochrome c oxidase subunit ...) x 9
  • Cox26
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / Cytochrome c oxidase Cytochrome bc1 Mitochondria Respiratory chain Supercomplex / OXIDOREDUCTASE / ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homologyCytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / 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 c oxidase subunit I domain / Cytochrome c oxidase, subunit VIa, conserved site / 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 b-c1 complex subunit 10, fungi / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome c oxidase subunit III-like superfamily / 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 / Cupredoxin / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome b/b6, C-terminal domain superfamily / Peptidase M16, C-terminal / 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 II, transmembrane domain 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 / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Rieske iron-sulphur protein, C-terminal / 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 / 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 c oxidase subunit III-like / Cytochrome oxidase c subunit VIb / Peptidase M16, zinc-binding site
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsHartley, A.M. / Pinotsis, N. / Marechal, A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc.
Authors: Andrew M Hartley / Natalya Lukoyanova / Yunyi Zhang / Alfredo Cabrera-Orefice / Susanne Arnold / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 5, 2018 / Release: Dec 26, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 26, 2018Structure modelrepositoryInitial release
1.1Jan 9, 2019Structure modelData collection / Database referencescitation / citation_author / pdbx_database_proc_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
1.2Jan 16, 2019Structure modelData collection / Database referencescitation / citation_author / pdbx_database_proc_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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
J: Cytochrome b-c1 complex subunit 10
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
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
l: Cox26
m: Cytochrome c oxidase subunit 1
n: Cytochrome c oxidase subunit 2
o: Cytochrome c oxidase subunit 3
p: Cytochrome c oxidase subunit 4, mitochondrial
q: Cytochrome c oxidase polypeptide 5A, mitochondrial
r: Cytochrome c oxidase subunit 6, mitochondrial
s: Cytochrome c oxidase subunit 7
t: Cytochrome c oxidase polypeptide VIII, mitochondrial
u: Cytochrome c oxidase subunit 7A
v: Cytochrome c oxidase subunit 6B
w: Cytochrome c oxidase subunit 6A, mitochondrial
x: Cox26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)936,427113
Polyers890,51444
Non-polymers45,91369
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#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: 47459.270 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 38751.918 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 20122.955 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 10856.314 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P37299

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Protein/peptide , 3 types, 6 molecules CNDOlx

#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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 27807.395 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07143
#22: Protein/peptide Cox26


Mass: 7461.718 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q2V2P9

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Cytochrome c oxidase subunit ... , 9 types, 18 molecules ambncodpfrgsiujvkw

#11: Protein/peptide Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I / COX1


Mass: 58832.586 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00401, cytochrome-c oxidase
#12: Protein/peptide Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II / COX2


Mass: 26779.816 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00410, cytochrome-c oxidase
#13: Protein/peptide Cytochrome c oxidase subunit 3 / / Cytochrome c oxidase polypeptide III / COX3


Mass: 30383.582 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00420, cytochrome-c oxidase
#14: Protein/peptide Cytochrome c oxidase subunit 4, mitochondrial / / Cytochrome c oxidase polypeptide IV / COX4


Mass: 14188.949 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04037, cytochrome-c oxidase
#16: Protein/peptide Cytochrome c oxidase subunit 6, mitochondrial / / Cytochrome c oxidase polypeptide VI / COX6


Mass: 12641.998 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00427, cytochrome-c oxidase
#17: Protein/peptide Cytochrome c oxidase subunit 7 / / Cytochrome c oxidase polypeptide VII / COX7


Mass: 6811.154 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10174, cytochrome-c oxidase
#19: Protein/peptide Cytochrome c oxidase subunit 7A / / Cytochrome c oxidase polypeptide VIIA / COX9


Mass: 6471.684 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07255, cytochrome-c oxidase
#20: Protein/peptide Cytochrome c oxidase subunit 6B / / Cytochrome c oxidase polypeptide VIb / COX12


Mass: 9668.697 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01519, cytochrome-c oxidase
#21: Protein/peptide Cytochrome c oxidase subunit 6A, mitochondrial / / Cytochrome c oxidase polypeptide VIa / COX13


Mass: 15117.017 Da / Num. of mol.: 2
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: COX13, YGL191W, G1341 / Production host: Saccharomyces cerevisiae (baker's yeast) / Strain (production host): W303-1B / References: UniProt: P32799, cytochrome-c oxidase

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Cytochrome c oxidase polypeptide ... , 2 types, 4 molecules eqht

#15: Protein/peptide Cytochrome c oxidase polypeptide 5A, mitochondrial / Cytochrome c oxidase polypeptide Va / COX5A


Mass: 14891.784 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P00424, cytochrome-c oxidase
#18: Protein/peptide Cytochrome c oxidase polypeptide VIII, mitochondrial


Mass: 5375.354 Da / Num. of mol.: 2
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04039, cytochrome-c oxidase

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Non-polymers , 13 types, 69 molecules

#23: Chemical...
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 28 / Formula: C37H74NO8P / Comment: phospholipid *YM
#24: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Formula: C34H32FeN4O4 / Heme
#25: 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.: 1 / Formula: C39H60O4
#26: 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.: 8 / Formula: C81H156O17P2 / Cardiolipin / Comment: phospholipid *YM
#27: Chemical
ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 8 / Formula: C40H80NO8P
#28: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Formula: C34H34FeN4O4 / Heme C
#29: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#30: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Formula: Cu / Copper
#31: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Formula: C49H56FeN4O6 / Heme A
#32: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#33: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / Magnesium
#34: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 4 / Formula: Cu2
#35: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: III2-IV2 mitochondrial respiratory supercomplex / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1B
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 92 % / Chamber temperature: 277.15 kelvins
Details: 3 microL of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec

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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 / Nominal magnification: 130000 / C2 aperture diameter: 70 microns
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 1.645 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansSampling size: 5 microns / Width: 3838 / Height: 3710

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIX1.13_2998model refinement
10RELION3.0initial Euler assignment
11RELION3.0final Euler assignment
12RELION3.0classification
13RELION3.03D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 44915 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11KYO1
21V541
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00864705
ELECTRON MICROSCOPYf_angle_d1.06987763
ELECTRON MICROSCOPYf_dihedral_angle_d17.85638221
ELECTRON MICROSCOPYf_chiral_restr0.0579460
ELECTRON MICROSCOPYf_plane_restr0.00810892

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