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- PDB-6zkc: Complex I during turnover, closed -

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Basic information

Entry
Database: PDB / ID: 6zkc
TitleComplex I during turnover, closed
Components
  • (Mitochondrial complex I, ...Respiratory complex I) x 16
  • (NADH dehydrogenase [ubiquinone] ...) x 8
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 2
  • (NADH:ubiquinone oxidoreductase subunit ...) x 10
  • Acyl carrier protein
KeywordsELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein
Function / homology
Function and homology information


blastocyst hatching / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport ...blastocyst hatching / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial large ribosomal subunit / electron transport chain / apoptotic mitochondrial changes / reactive oxygen species metabolic process / respirasome / respiratory electron transport chain / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / brain development / mitochondrial inner membrane / response to oxidative stress / nuclear body / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / integral component of membrane / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
Tim17/Tim22/Tim23/Pmp24 family / 2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) ...Tim17/Tim22/Tim23/Pmp24 family / 2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH:ubiquinone oxidoreductase, chain 2 / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase subunit 2 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase, chain G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH:ubiquinone oxidoreductase, subunit G / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Deoxynucleoside kinase domain / Deoxynucleoside kinase / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain 5-like / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Soluble ligand binding domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / SLBB domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like
Similarity search - Domain/homology
Complex I-15 kDa / Complex I-ESSS / NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.7 / Complex I-30kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-B22 / NADH:ubiquinone oxidoreductase subunit A9 / Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial ...Complex I-15 kDa / Complex I-ESSS / NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B14.7 / Complex I-30kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-B22 / NADH:ubiquinone oxidoreductase subunit A9 / Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-B14.5a / Complex I-B17 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-B12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-AGGG / Complex I-B14 / Complex I-B15 / Complex I-B18 / 1,2-Distearoyl-sn-glycerophosphoethanolamine / Complex I-B9 / IRON/SULFUR CLUSTER / CARDIOLIPIN / Chem-DCQ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / : / MYRISTIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-ZMP / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / ADENOSINE MONOPHOSPHATE / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / 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 / Complex I-SGDH
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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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Structure visualization

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Assembly

Deposited unit
1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
2: Mitochondrial complex I, 24 kDa subunit
3: NADH:ubiquinone oxidoreductase core subunit S1
4: Mitochondrial complex I, 49 kDa subunit
5: NADH:ubiquinone oxidoreductase core subunit S3
6: Mitochondrial complex I, PSST subunit
9: Mitochondrial complex I, TYKY subunit
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
a: Mitochondrial complex I, 10 kDa subunit
b: Mitochondrial complex I, 13 kDa subunit
c: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
d: NADH:ubiquinone oxidoreductase subunit A9
e: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
f: Mitochondrial complex I, B13 subunit
g: NADH:ubiquinone oxidoreductase subunit A6
h: Mitochondrial complex I, B14.5a subunit
i: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
j: Acyl carrier protein
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,080,81590
Polymers1,048,63645
Non-polymers32,17945
Water0
1


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

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Components

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NADH dehydrogenase [ubiquinone] ... , 8 types, 8 molecules 1Yceikov

#1: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50687.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#18: 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
#22: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 19381.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PE07
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QAH8
#28: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: B9VGZ9
#29: 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
#33: 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
#40: 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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Mitochondrial complex I, ... , 16 types, 16 molecules 2469VZabfhqrwxyz

#2: Protein Mitochondrial complex I, 24 kDa subunit


Mass: 27373.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NRY1
#4: Protein Mitochondrial complex I, 49 kDa subunit


Mass: 52661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#6: Protein Mitochondrial complex I, PSST subunit


Mass: 24622.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#7: Protein Mitochondrial complex I, TYKY subunit


Mass: 24496.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#15: 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
#19: 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)
#20: Protein Mitochondrial complex I, 10 kDa subunit


Mass: 11916.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#21: Protein Mitochondrial complex I, 13 kDa subunit


Mass: 13457.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#25: Protein Mitochondrial complex I, B13 subunit


Mass: 13287.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PNX7
#27: Protein Mitochondrial complex I, B14.5a subunit


Mass: 12701.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P0I2
#35: 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)
#36: 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
#41: 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
#42: 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)
#43: 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)
#44: 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)

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NADH:ubiquinone oxidoreductase core subunit ... , 2 types, 2 molecules 35

#3: Protein NADH:ubiquinone oxidoreductase core subunit S1


Mass: 79519.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QB34
#5: Protein NADH:ubiquinone oxidoreductase core subunit S3


Mass: 30384.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PB27

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

#8: 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)
#9: 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)
#10: 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)
#11: 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)
#12: 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)
#13: 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)
#14: 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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NADH:ubiquinone oxidoreductase subunit ... , 10 types, 10 molecules Wdglmnpstu

#16: 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
#23: Protein NADH:ubiquinone oxidoreductase subunit A9 /


Mass: 43025.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PI58
#26: Protein NADH:ubiquinone oxidoreductase subunit A6 /


Mass: 16302.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QC06
#30: 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
#31: 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
#32: 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
#34: 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
#37: 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
#38: 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
#39: 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, 2 molecules Xj

#17: Protein Acyl carrier protein /


Mass: 17608.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NQT7

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Non-polymers , 14 types, 45 molecules

#45: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#46: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#47: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#48: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#49: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#50: Chemical ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H30O4
#51: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#52: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#53: 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.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#54: 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.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#56: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#57: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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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: Complex I during turnover, closed / Type: COMPLEX / Entity ID: #1-#44 / 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
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

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
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15769 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5LNK

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