[English] 日本語
Yorodumi
- PDB-8zou: Respirasome open state 2 in presence of metformin (SC-MetO2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zou
TitleRespirasome open state 2 in presence of metformin (SC-MetO2)
Components
  • (Cytochrome b-c1 complex subunit ...) x 7
  • (Cytochrome c oxidase ...) x 13
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 11
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 10
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 5
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • Acyl carrier protein
  • Complex I-30kD
  • Complex I-49kD
  • Complex I-9kD
  • Complex I-B14.5a
  • Complex I-B17
  • Complex III subunit 9
  • Cytochrome b
  • Cytochrome c domain-containing protein
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
KeywordsMEMBRANE PROTEIN / Metformin / electron transport chain / Respirasome / mammalia
Function / homology
Function and homology information


Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / respiratory chain complex IV assembly / Mitochondrial protein import / subthalamus development / pons development ...Mitochondrial Fatty Acid Beta-Oxidation / Protein lipoylation / Complex IV assembly / Cytoprotection by HMOX1 / TP53 Regulates Metabolic Genes / Complex III assembly / respiratory chain complex IV assembly / Mitochondrial protein import / subthalamus development / pons development / : / mitochondrial respirasome assembly / RHOG GTPase cycle / cerebellar Purkinje cell layer development / Complex I biogenesis / : / Respiratory electron transport / pyramidal neuron development / respiratory chain complex IV / thalamus development / Mitochondrial protein degradation / Neutrophil degranulation / mesenchymal stem cell proliferation / respiratory chain complex / reproductive system development / mitochondrial [2Fe-2S] assembly complex / mitochondrial large ribosomal subunit binding / cytochrome-c oxidase / respiratory chain complex III / mesenchymal stem cell differentiation / circulatory system development / oxidative phosphorylation / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / cardiac muscle tissue development / [2Fe-2S] cluster assembly / oxidoreductase activity, acting on NAD(P)H / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / stem cell division / mitochondrial electron transport, ubiquinol to cytochrome c / hypothalamus development / midbrain development / acyl binding / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / response to cAMP / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / enzyme regulator activity / muscle contraction / reactive oxygen species metabolic process / aerobic respiration / central nervous system development / regulation of mitochondrial membrane potential / respiratory electron transport chain / hippocampus development / DNA damage response, signal transduction by p53 class mediator / kidney development / electron transport chain / fatty acid metabolic process / brain development / metalloendopeptidase activity / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / multicellular organism growth / NAD binding / cellular senescence / FMN binding / nervous system development / 4 iron, 4 sulfur cluster binding / gene expression / oxidoreductase activity / mitochondrial inner membrane / nuclear speck / nuclear body / mitochondrial matrix / copper ion binding / heme binding / structural molecule activity / mitochondrion / proteolysis / nucleoplasm / metal ion binding / membrane
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / : / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome c/quinol oxidase subunit II / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / : / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c oxidase, subunit I, copper-binding site / : / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / : / Cytochrome c oxidase subunit I / Cytochrome b/b6, C-terminal / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome b(C-terminal)/b6/petD / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome b/b6, C-terminal domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP ...1,2-Distearoyl-sn-glycerophosphoethanolamine / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / COPPER (II) ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PLX / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / Acyl carrier protein / Cytochrome c oxidase subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / Cytochrome c oxidase subunit 4 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / Cytochrome c oxidase subunit / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c oxidase subunit 6C / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Cytochrome b-c1 complex subunit 10 / Cytochrome c oxidase subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / : / Cytochrome b-c1 complex subunit 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Cytochrome b-c1 complex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Cytochrome b-c1 complex subunit 6 / 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 / Cytochrome c oxidase subunit 5A, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / Cytochrome c oxidase subunit 1 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 6 / Cytochrome c oxidase subunit 2 / NADH-ubiquinone oxidoreductase chain 4L / Cytochrome b / Cytochrome c oxidase subunit 7C, mitochondrial / Complex III subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 5B, mitochondrial / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / Cytochrome c oxidase subunit 7A1, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsTeng, F. / He, Z.X. / Hu, Y.Q. / Xu, C.Y. / Guo, R.Y. / Zhou, L.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZJU100 Young Professor China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Hydrophilic metformin and hydrophobic biguanides inhibit mitochondrial complex I by distinct mechanisms.
Authors: Zhaoxiang He / Fei Teng / Yanqing Yang / Ruiyang Guo / Mengchen Wu / Fangzhu Han / Hongtao Tian / Jiawei Wang / Yiqi Hu / Yangwei Jiang / Leili Zhang / Chenyang Xu / Fan Yang / Jiancang Zhou ...Authors: Zhaoxiang He / Fei Teng / Yanqing Yang / Ruiyang Guo / Mengchen Wu / Fangzhu Han / Hongtao Tian / Jiawei Wang / Yiqi Hu / Yangwei Jiang / Leili Zhang / Chenyang Xu / Fan Yang / Jiancang Zhou / Shan Zhang / James A Letts / Ruhong Zhou / Long Zhou /
Abstract: Metformin is the only antihyperglycemic biguanide targeting type 2 diabetes mellitus with proven safety. Although a mechanism of action involving tight inhibition of the respiratory complex I has ...Metformin is the only antihyperglycemic biguanide targeting type 2 diabetes mellitus with proven safety. Although a mechanism of action involving tight inhibition of the respiratory complex I has been proposed for hydrophobic biguanides, it remains elusive for the hydrophilic metformin, whose excellent pharmacological tolerance depends on weak complex I inhibition without competitive nature. Here we solved cryo-electron microscopy structures of the metformin-bound porcine respirasome. Our structural and kinetic data are consistent with a model in which metformin enters complex I only in its open state and becomes trapped at the ubiquinone redox site by ubiquinone-induced conformational closing of the enzyme. By contrast, the hydrophobic proguanil alone occupies both the entrance and the redox site of the ubiquinone channel in open and closed complex I and is kinetically consistent with competitive inhibition with conformation-dependent affinities. Our data provide the molecular basis for metformin's well-known superior properties, such as a wide therapeutic window and positive ubiquinone cooperativity, leading to its clinical success and facilitating future therapeutic developments.
History
DepositionMay 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
4L: NADH-ubiquinone oxidoreductase chain 4L
5A: Cytochrome c oxidase subunit 5A, mitochondrial
5B: Cytochrome c oxidase subunit 5B, mitochondrial
6A: Cytochrome c oxidase subunit
6B: Cytochrome c oxidase subunit
6C: Cytochrome c oxidase subunit 6C
7A: Cytochrome c oxidase subunit 7A1, mitochondrial
7B: Cytochrome c oxidase subunit 7B, mitochondrial
7C: Cytochrome c oxidase subunit 7C, mitochondrial
8B: Cytochrome c oxidase subunit 8
A1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
A2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
A3: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
A5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
A6: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
A7: Complex I-B14.5a
A8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
A9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
AB: Acyl carrier protein
AC: Acyl carrier protein
AK: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
AM: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
AN: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
B1: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
B2: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial
B3: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
B4: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
B5: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
B6: Complex I-B17
B7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
B8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
B9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
BK: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
BL: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
C1: Cytochrome c oxidase subunit 1
C2: Cytochrome c oxidase subunit 2
C3: Cytochrome c oxidase subunit 3
C4: Cytochrome c oxidase subunit 4
CA: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
CB: NADH dehydrogenase [ubiquinone] 1 subunit C2
N1: NADH-ubiquinone oxidoreductase chain 1
N2: NADH-ubiquinone oxidoreductase chain 2
N3: NADH-ubiquinone oxidoreductase chain 3
N4: NADH-ubiquinone oxidoreductase chain 4
N5: NADH-ubiquinone oxidoreductase chain 5
N6: NADH-ubiquinone oxidoreductase chain 6
QA: Cytochrome b-c1 complex subunit 2, mitochondrial
QB: Cytochrome b-c1 complex subunit 1, mitochondrial
QC: Cytochrome b
QD: Cytochrome c domain-containing protein
QE: Cytochrome b-c1 complex subunit Rieske, mitochondrial
QF: Cytochrome b-c1 complex subunit 6
QG: Cytochrome b-c1 complex subunit 7
QH: Cytochrome b-c1 complex subunit 8
QI: Complex III subunit 9
QJ: Cytochrome b-c1 complex subunit 10
QK: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Qa: Cytochrome b-c1 complex subunit 2, mitochondrial
Qb: Cytochrome b-c1 complex subunit 1, mitochondrial
Qc: Cytochrome b
Qd: Cytochrome c domain-containing protein
Qe: Cytochrome b-c1 complex subunit Rieske, mitochondrial
Qf: Cytochrome b-c1 complex subunit 6
Qg: Cytochrome b-c1 complex subunit 7
Qh: Cytochrome b-c1 complex subunit 8
Qi: Complex III subunit 9
Qj: Cytochrome b-c1 complex subunit 10
S1: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
S2: Complex I-49kD
S3: Complex I-30kD
S4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
S5: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
S6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
S8: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
V2: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
V3: Complex I-9kD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,768,714206
Polymers1,666,52179
Non-polymers102,194127
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

+
NADH-ubiquinone oxidoreductase chain ... , 7 types, 7 molecules 4LN1N2N3N4N5N6

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


Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating)
#42: 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)
#43: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 12869.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79880, NADH:ubiquinone reductase (H+-translocating)
#44: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 51853.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q7IIB7, NADH:ubiquinone reductase (H+-translocating)
#45: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 68267.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q71K68, NADH:ubiquinone reductase (H+-translocating)
#46: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 18890.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating)

+
Cytochrome c oxidase ... , 13 types, 13 molecules 5A5B6A6B6C7A7B7C8BC1C2C3C4

#2: Protein Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome c oxidase polypeptide Va


Mass: 11717.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJ34
#3: Protein Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase polypeptide Vb


Mass: 10382.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q5S3G4
#4: Protein Cytochrome c oxidase subunit / Cytochrome c oxidase polypeptide VIa


Mass: 8724.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEB7
#5: Protein Cytochrome c oxidase subunit


Mass: 9723.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TG97
#6: Protein Cytochrome c oxidase subunit 6C / Cytochrome c oxidase polypeptide VIc


Mass: 8139.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TXH1
#7: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome c oxidase subunit VIIa-heart / Cytochrome c oxidase subunit VIIa-H


Mass: 6376.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q8SPJ9
#8: Protein/peptide Cytochrome c oxidase subunit 7B, mitochondrial / Cytochrome c oxidase polypeptide VIIb


Mass: 5543.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BJ57
#9: Protein/peptide Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase polypeptide VIIc


Mass: 5465.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1W0Y2
#10: Protein/peptide Cytochrome c oxidase subunit 8 / Cytochrome c oxidase polypeptide VIII


Mass: 4776.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VY94
#35: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 56992.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79876, cytochrome-c oxidase
#36: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II


Mass: 26203.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P50667, cytochrome-c oxidase
#37: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 29753.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q35916, cytochrome-c oxidase
#38: Protein Cytochrome c oxidase subunit 4


Mass: 16323.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T8J9

+
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 11 types, 11 molecules A1A2A3A5A6A8A9AKALAMAN

#11: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Complex I-MWFE / NADH-ubiquinone oxidoreductase MWFE subunit


Mass: 8034.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 9770.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RGE3
#13: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / Complex I-B9 / NADH-ubiquinone oxidoreductase B9 subunit


Mass: 9094.372 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VPG4
#14: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5


Mass: 12949.106 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1IJ52
#15: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / Complex I-B14 / NADH-ubiquinone oxidoreductase B14 subunit


Mass: 13755.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SJP6
#17: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH-ubiquinone oxidoreductase 19 kDa subunit / Complex I-19kD


Mass: 19932.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1
#18: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / Complex I-39kD / NADH-ubiquinone oxidoreductase 39 kDa subunit


Mass: 38840.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL07
#20: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 36792.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9
#21: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase subunit B14.7 / Complex I-B14.7


Mass: 14555.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17031.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SQP4
#23: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16709.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1NRT6

+
Protein , 9 types, 13 molecules A7ABACB6QCQcQDQdQIQiS1S2S3

#16: Protein Complex I-B14.5a / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase subunit B14.5a


Mass: 12517.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VLA2
#19: Protein Acyl carrier protein


Mass: 17308.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AAR5
#29: Protein Complex I-B17 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH-ubiquinone oxidoreductase B17 subunit


Mass: 15333.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN80
#49: Protein Cytochrome b


Mass: 42840.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q1HBG9
#50: Protein Cytochrome c domain-containing protein


Mass: 27373.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0K1H3
#55: Protein Complex III subunit 9


Mass: 7281.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN79
#57: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial


Mass: 75683.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1F3I4
#58: Protein Complex I-49kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / mitochondrial / NADH-ubiquinone ...NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / mitochondrial / NADH-ubiquinone oxidoreductase 49 kDa subunit


Mass: 49234.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JYS1
#59: Protein Complex I-30kD / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / mitochondrial / NADH-ubiquinone ...NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / mitochondrial / NADH-ubiquinone oxidoreductase 30 kDa subunit


Mass: 24521.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNN4

+
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ... , 10 types, 10 molecules B1B2B3B4B5B7B8B9BKBL

#24: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / Complex I-MNLL / NADH-ubiquinone oxidoreductase MNLL subunit


Mass: 6781.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D2CGH8
#25: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / Complex I-AGGG / NADH-ubiquinone oxidoreductase AGGG subunit


Mass: 8201.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QW32
#26: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-B12 / NADH-ubiquinone oxidoreductase B12 subunit


Mass: 9042.212 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VD84
#27: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH-ubiquinone oxidoreductase B15 subunit / Complex I-B15


Mass: 14986.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0
#28: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH-ubiquinone oxidoreductase SGDH subunit / Complex I-SGDH


Mass: 16281.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6
#30: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Complex I-B18 / NADH-ubiquinone oxidoreductase B18 subunit


Mass: 15307.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1
#31: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18608.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7
#32: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 21733.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GSE5
#33: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase PDSW subunit / Complex I-PDSW


Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYV0
#34: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / Complex I-ESSS / NADH-ubiquinone oxidoreductase ESSS subunit


Mass: 12113.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1EYI7

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

#39: Protein/peptide NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase KFYI subunit / Complex I-KFYI


Mass: 5881.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQS6
#40: Protein NADH dehydrogenase [ubiquinone] 1 subunit C2


Mass: 14196.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3

+
Cytochrome b-c1 complex subunit ... , 7 types, 15 molecules QAQaQBQbQEQKQeQFQfQGQgQHQhQJQj

#47: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Ubiquinol-cytochrome c reductase core protein 2


Mass: 44727.215 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RPD2
#48: Protein Cytochrome b-c1 complex subunit 1, mitochondrial


Mass: 49270.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0PK14
#51: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 29492.600 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A4X1TWD8, quinol-cytochrome-c reductase
#52: Protein Cytochrome b-c1 complex subunit 6


Mass: 7933.944 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S3W0
#53: Protein Cytochrome b-c1 complex subunit 7


Mass: 12644.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1U2M7
#54: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8


Mass: 9653.144 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UYT9
#56: Protein Cytochrome b-c1 complex subunit 10


Mass: 6058.093 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VTU3

+
NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 5 types, 5 molecules S4S5S6S7S8

#60: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 14314.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1SN37
#61: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH-ubiquinone oxidoreductase 15 kDa subunit / Complex I-15 kDa


Mass: 12375.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23
#62: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 10567.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S031
#63: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Complex I-20kD / NADH-ubiquinone oxidoreductase 20 kDa subunit


Mass: 17874.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1J578
#64: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH-ubiquinone oxidoreductase 23 kDa subunit / Complex I-23kD


Mass: 20207.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BDC0

+
NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2

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


Mass: 47235.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A4X1SZP7, NADH:ubiquinone reductase (H+-translocating)
#66: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 23826.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BG40

+
Protein/peptide , 1 types, 1 molecules V3

#67: Protein/peptide Complex I-9kD / NADH dehydrogenase [ubiquinone] flavoprotein 3 / mitochondrial / NADH-ubiquinone oxidoreductase 9 kDa subunit


Mass: 5046.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TFI3

+
Non-polymers , 18 types, 127 molecules

#68: 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.: 24 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#69: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#70: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#71: Chemical...
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#72: 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.: 6 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#73: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#74: 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 / Feature type: SUBJECT OF INVESTIGATION
#75: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#76: Chemical
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C42H89NO8P / Comment: phospholipid*YM
#77: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#78: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#79: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#80: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#81: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#82: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#83: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H52O8P
#84: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#85: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P

+
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Respirasome open state 2 in presence of metformin / Type: COMPLEX / Entity ID: #1-#67 / Source: NATURAL
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.4
Details: SEC buffer (20 mM Tris pH 7.4, 50 mM NaCl, 0.002% PMSF, 0.1% GDN (w/v))
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrimethylsilylTris1
250 mMSodium chlorideNaCl1
30.002 %PhenylmethylsulfonylPMSF1
40.1 %Glyco-diosgeninGDN1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

-
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 magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.8 sec. / Electron dose: 51.9 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7PHENIX1.20.1model fitting
8Coot0.9.6model fitting
10cryoSPARCv4.4.1initial Euler assignment
11cryoSPARCv4.4.1final Euler assignment
12cryoSPARCv4.4.1classification
13cryoSPARCv4.4.13D reconstruction
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250490 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 123.44 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033121337
ELECTRON MICROSCOPYf_angle_d0.5134163663
ELECTRON MICROSCOPYf_chiral_restr0.041817411
ELECTRON MICROSCOPYf_plane_restr0.004220190
ELECTRON MICROSCOPYf_dihedral_angle_d12.67347131

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more