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- PDB-6zka: Membrane domain of open complex I during turnover -

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Entry
Database: PDB / ID: 6zka
TitleMembrane domain of open complex I during turnover
Components
  • (Mitochondrial complex I, ...Respiratory complex I) x 9
  • (NADH dehydrogenase [ubiquinone] 1 ...) x 4
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase subunit ...) x 8
  • Acyl carrier protein
KeywordsELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / reactive oxygen species metabolic process / mitochondrial intermembrane space ...NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / reactive oxygen species metabolic process / mitochondrial intermembrane space / fatty acid biosynthetic process / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrial matrix
Similarity search - Function
NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 ...NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Complex 1 LYR protein domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / Complex 1 protein (LYR family) / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE MONOPHOSPHATE / CARDIOLIPIN / Chem-DCQ / MYRISTIC ACID / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE MONOPHOSPHATE / CARDIOLIPIN / Chem-DCQ / MYRISTIC ACID / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKampjut, D. / Sazanov, L.A.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Commission665385European Union
European Commission653706European Union
CitationJournal: Science / Year: 2020
Title: The coupling mechanism of mammalian respiratory complex I.
Authors: Domen Kampjut / Leonid A Sazanov /
Abstract: Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
H: NADH-ubiquinone oxidoreductase chain 1
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH-ubiquinone oxidoreductase chain 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH-ubiquinone oxidoreductase chain 2
V: Mitochondrial complex I, B14.7 subunit
W: NADH:ubiquinone oxidoreductase subunit B5
X: Acyl carrier protein
Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Z: Mitochondrial complex I, PDSW subunit
k: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
l: NADH:ubiquinone oxidoreductase subunit S5
m: NADH:ubiquinone oxidoreductase subunit A3
n: NADH:ubiquinone oxidoreductase subunit B3
o: NADH dehydrogenase [ubiquinone] 1 subunit C2
p: NADH:ubiquinone oxidoreductase subunit B4
q: Mitochondrial complex I, B16.6 subunit
r: Mitochondrial complex I, B17 subunit
s: NADH:ubiquinone oxidoreductase subunit B7
t: NADH:ubiquinone oxidoreductase subunit B9
u: NADH:ubiquinone oxidoreductase subunit B2
v: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
w: Mitochondrial complex I, ESSS subunit
x: Mitochondrial complex I, KFYI subunit
y: Mitochondrial complex I, MNLL subunit
z: Mitochondrial complex I, MWFE subunit
4: Mitochondrial complex I, ND4L subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)660,27357
Polymers635,63029
Non-polymers24,64328
Water23,2931293
1


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

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Components

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules AHJKLMN

#1: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78753, NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78747, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78757, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10868.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78754, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68438.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78756, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 52086.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78755, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39149.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: O78748, NADH:ubiquinone reductase (H+-translocating)

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Mitochondrial complex I, ... , 9 types, 9 molecules VZqrwxyz4

#8: Protein Mitochondrial complex I, B14.7 subunit


Mass: 14784.009 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PAR2
#12: Protein Mitochondrial complex I, PDSW subunit


Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#19: Protein Mitochondrial complex I, B16.6 subunit


Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#20: Protein Mitochondrial complex I, B17 subunit


Mass: 15565.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PZE3
#25: Protein Mitochondrial complex I, ESSS subunit


Mass: 17410.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PWF1
#26: Protein Mitochondrial complex I, KFYI subunit


Mass: 8802.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#27: Protein Mitochondrial complex I, MNLL subunit


Mass: 7075.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#28: Protein Mitochondrial complex I, MWFE subunit


Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#29: Protein Mitochondrial complex I, ND4L subunit


Mass: 52634.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)

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NADH:ubiquinone oxidoreductase subunit ... , 8 types, 8 molecules Wlmnpstu

#9: Protein NADH:ubiquinone oxidoreductase subunit B5 /


Mass: 21614.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QHN8
#14: Protein NADH:ubiquinone oxidoreductase subunit S5 /


Mass: 12605.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QFF9
#15: Protein NADH:ubiquinone oxidoreductase subunit A3 /


Mass: 9325.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NYM7
#16: Protein NADH:ubiquinone oxidoreductase subunit B3 /


Mass: 11146.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q5T4
#18: Protein NADH:ubiquinone oxidoreductase subunit B4 /


Mass: 15236.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QF73
#21: Protein NADH:ubiquinone oxidoreductase subunit B7 /


Mass: 16413.807 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P5V3
#22: Protein NADH:ubiquinone oxidoreductase subunit B9 /


Mass: 21779.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PGA3
#23: Protein NADH:ubiquinone oxidoreductase subunit B2 /


Mass: 12226.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PVD7

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Protein , 1 types, 1 molecules X

#10: Protein Acyl carrier protein /


Mass: 17608.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NQT7

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NADH dehydrogenase [ubiquinone] 1 ... , 4 types, 4 molecules Ykov

#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20139.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PYA5
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40557.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QBF5
#17: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14431.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P9Q8
#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 21752.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q1B0

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Non-polymers , 8 types, 1321 molecules

#30: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C44H88NO8P / Comment: phospholipid*YM
#31: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H30O4 / Source: (natural) Ovis aries (sheep)
#32: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#33: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#34: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#35: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#36: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#37: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1293 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: Membrane domain of open complex I during turnover / Type: COMPLEX / Entity ID: #1-#29 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.15CTF correction
7Coot0.8.9model fitting
9PHENIX1.12model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315484 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5LNK

5lnk

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00840538
ELECTRON MICROSCOPYf_angle_d0.99654705
ELECTRON MICROSCOPYf_dihedral_angle_d10.40524584
ELECTRON MICROSCOPYf_chiral_restr0.0625922
ELECTRON MICROSCOPYf_plane_restr0.0086678

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