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- PDB-8ueo: In-situ complex I (Active-Apo) -

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Entry
Database: PDB / ID: 8ueo
TitleIn-situ complex I (Active-Apo)
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH:ubiquinone oxidoreductase subunit ...) x 4
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsELECTRON TRANSPORT / in-situ cryo-EM structure / mammalian / mitochondria / respiratory supercomplex / proton pumping / membrane protein
Function / homology
Function and homology information


RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / deoxynucleoside kinase activity / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / cellular respiration ...RHOG GTPase cycle / Complex I biogenesis / Respiratory electron transport / Neutrophil degranulation / Mitochondrial protein degradation / deoxynucleoside kinase activity / cardiac muscle tissue development / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / cellular respiration / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / ubiquinone binding / mitochondrial respiratory chain complex I assembly / acyl binding / NADH dehydrogenase (ubiquinone) activity / acyl carrier activity / electron transport coupled proton transport / quinone binding / ATP synthesis coupled electron transport / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / electron transport chain / regulation of protein phosphorylation / brain development / mitochondrial intermembrane space / negative regulation of cell growth / 2 iron, 2 sulfur cluster binding / NAD binding / positive regulation of fibroblast proliferation / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / nuclear body / mitochondrial matrix / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family ...NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Tim17/Tim22/Tim23/Pmp24 family / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase 1 beta subcomplex subunit 2 / Zinc finger, CHCC-type / Zinc-finger domain / 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 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / 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 / NDUFA6, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Deoxynucleoside kinase domain / Deoxynucleoside kinase / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 LYR protein domain / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Complex 1 protein (LYR family) / 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, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-TRIPHOSPHATE / : / MYRISTIC ACID / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / GUANOSINE-5'-TRIPHOSPHATE / : / MYRISTIC ACID / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH:ubiquinone oxidoreductase subunit V3 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 5
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZheng, W. / Zhu, J. / Zhang, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM142959 United States
CitationJournal: Nature / Year: 2024
Title: High-resolution in situ structures of mammalian respiratory supercomplexes.
Authors: Wan Zheng / Pengxin Chai / Jiapeng Zhu / Kai Zhang /
Abstract: Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in ...Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: IIIIIV, IIIIIV, IIIIIV and IIIIIV, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
History
DepositionOct 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
1A: NADH-ubiquinone oxidoreductase chain 3
1B: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
1C: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
1D: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
1E: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
1F: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
1G: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
1H: NADH-ubiquinone oxidoreductase chain 1
1I: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
1J: NADH-ubiquinone oxidoreductase chain 6
1K: NADH-ubiquinone oxidoreductase chain 4L
1L: NADH-ubiquinone oxidoreductase chain 5
1M: NADH-ubiquinone oxidoreductase chain 4
1N: NADH-ubiquinone oxidoreductase chain 2
1O: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
1P: NADH:ubiquinone oxidoreductase subunit A9
1Q: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
1R: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
1S: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
1T: NADH:ubiquinone oxidoreductase subunit AB1
1U: NADH:ubiquinone oxidoreductase subunit AB1
1V: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1
1W: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
1X: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
1Y: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
1Z: NADH:ubiquinone oxidoreductase subunit A13
1a: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
1b: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
1c: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
1d: NADH dehydrogenase [ubiquinone] 1 subunit C2
1e: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
1f: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus scrofa]
1g: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
1h: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
1i: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
1j: NADH:ubiquinone oxidoreductase subunit B2
1k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
1l: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
1m: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
1n: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
1o: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
1p: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
1q: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
1r: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
1s: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,129,81891
Polymers1,097,56845
Non-polymers32,25046
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 1A1H1J1K1L1M1N

#1: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 12998.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79880
#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 35591.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A0U1RS44, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6


Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79882
#11: Protein NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase subunit 4L


Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 68695.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q9TDR1, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 51859.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79881, NADH:ubiquinone reductase (H+-translocating)
#14: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating)

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 7 types, 7 molecules 1B1C1D1I1Q1R1e

#2: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 28500.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VVS8
#3: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial


Mass: 30154.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4
#4: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial


Mass: 54168.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0QM68
#9: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial


Mass: 27135.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZUN9
#17: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 19746.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SN37
#18: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 13348.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1THU2
#30: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5


Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VX77

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 3 types, 3 molecules 1E1F1s

#5: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 27439.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VRV3
#6: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50637.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SZP7
#44: Protein NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial


Mass: 48217.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TE42

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Protein , 1 types, 1 molecules 1G

#7: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 79627.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ARY3

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 10 types, 10 molecules 1O1S1V1W1X1Y1a1b1q1r

#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#19: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11099.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1FN21
#21: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 isoform X1


Mass: 13321.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0UWW0
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14953.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480VKQ8
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K6B5
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11


Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 8034.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0TJQ4
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3


Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VQ42
#42: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17162.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#43: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7


Mass: 12648.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8W4F7N8

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NADH:ubiquinone oxidoreductase subunit ... , 4 types, 5 molecules 1P1T1U1Z1j

#16: Protein NADH:ubiquinone oxidoreductase subunit A9


Mass: 42606.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULW2
#20: Protein NADH:ubiquinone oxidoreductase subunit AB1


Mass: 17338.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1KH26
#25: Protein NADH:ubiquinone oxidoreductase subunit A13


Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K655
#35: Protein NADH:ubiquinone oxidoreductase subunit B2


Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1G9F4

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NADH dehydrogenase [ubiquinone] 1 subunit ... , 2 types, 2 molecules 1c1d

#28: Protein NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial


Mass: 8664.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYQ2
#29: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14353.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3

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NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 10 molecules 1f1g1h1i1k1l1m1n1o1p

#31: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 [Sus scrofa]


Mass: 15371.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1IZ33
#32: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial


Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYI7
#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial


Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#34: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6


Mass: 15645.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UIV8
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3


Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VD84
#37: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial


Mass: 21658.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: B8Y651
#38: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0
#39: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9


Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#40: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 16487.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1
#41: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10


Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0R7A9

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Non-polymers , 13 types, 46 molecules

#45: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#46: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#47: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#48: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#49: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#50: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#51: 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.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#52: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#53: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#54: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#55: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#56: Chemical ChemComp-EHZ / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate


Mass: 584.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O9PS
#57: Chemical ChemComp-MYR / MYRISTIC ACID


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

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Details

Has ligand of interestY

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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: In-situ cryo-EM structure of respiratory supercomplex by directly imaging mitochondria
Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00869724
ELECTRON MICROSCOPYf_angle_d1.13994355
ELECTRON MICROSCOPYf_dihedral_angle_d7.20510225
ELECTRON MICROSCOPYf_chiral_restr0.05610261
ELECTRON MICROSCOPYf_plane_restr0.00811816

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