[English] 日本語
Yorodumi
- PDB-9f62: Subtomogram average of the Chlamydomonas reinhardtii mitochondria... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f62
TitleSubtomogram average of the Chlamydomonas reinhardtii mitochondrial respirasome I2 III4 IV6
Components
  • (Cytochrome b-c1 complex subunit ...) x 3
  • (Cytochrome c oxidase ...) x 4
  • (Mitochondrial NADH:ubiquinone oxidoreductase ...) x 9
  • (Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] ...) x 6
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • (NADH:ubiquinone oxidoreductase ...) x 11
  • (Putative NADH:ubiquinone oxidoreductase ...) x 3
  • AGGG
  • ASHI
  • Acyl carrier protein
  • Alpha-MPP
  • B14.5a
  • B9
  • CAG1
  • CAG2 - CA-like
  • Complex III subunit 9
  • Cox5b
  • Cox5c
  • Cox6a
  • Cox6b
  • Cox7a
  • Cox7c
  • CoxIn
  • Cytochrome b
  • Cytochrome c1
  • ESSS
  • KFYI
  • MPP-Beta
  • Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit
  • NADH dehydrogenase subunit 4L
  • NUOP7
  • NUOP8
  • P10
  • P9
  • cytochrome-c oxidase
KeywordsMEMBRANE PROTEIN / respirasome / alga / respiration / mitochondria
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / TIM22 mitochondrial import inner membrane insertion complex / quinol-cytochrome-c reductase / NADH dehydrogenase / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / ubiquinone biosynthetic process / respiratory chain complex IV / mitochondrial envelope ...NADH:ubiquinone reductase (H+-translocating) / TIM22 mitochondrial import inner membrane insertion complex / quinol-cytochrome-c reductase / NADH dehydrogenase / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / ubiquinone biosynthetic process / respiratory chain complex IV / mitochondrial envelope / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / oxidoreductase activity, acting on NAD(P)H / mitochondrial electron transport, cytochrome c to oxygen / ubiquinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / acyl binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / phosphopantetheine binding / protein transmembrane transporter activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / electron transfer activity / mitochondrial inner membrane / copper ion binding / heme binding / protein-containing complex binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Mitochondrial import inner membrane translocase subunit TIM22 / Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / : / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Cytochrome c oxidase, subunit VIb ...Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Mitochondrial import inner membrane translocase subunit TIM22 / Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / : / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit III domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b-c1 complex subunit 7 / Cytochrome c oxidase subunit III / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / 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 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c/quinol oxidase subunit II / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Hexapeptide repeat / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome b/b6, C-terminal / Cytochrome c oxidase-like, subunit I domain / Cytochrome b(C-terminal)/b6/petD / Cytochrome oxidase subunit I profile. / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Tim17/Tim22/Tim23/Pmp24 family / Bacterial transferase hexapeptide (six repeats) / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Peptidase M16, C-terminal / Peptidase M16 inactive domain / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / 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 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region
Similarity search - Domain/homology
Chem-8Q1 / CROTONYL COENZYME A / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP ...Chem-8Q1 / CROTONYL COENZYME A / COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / IRON/SULFUR CLUSTER / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome b-c1 complex subunit 7 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8 / Uncharacterized protein / Uncharacterized protein / Cytochrome b-c1 complex subunit 6 / Uncharacterized protein / Complex III subunit 9 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome c oxidase subunit 1 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4 / Cytochrome b / Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit / Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit / Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit / Acyl carrier protein / NADH:ubiquinone oxidoreductase 78 kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase B14 subunit / NADH:ubiquinone oxidoreductase 20,9 kD-like subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH:ubiquinone oxidoreductase 13 kD-like subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase chain 3 / Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit / Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit / Putative NADH:ubiquinone oxidoreductase 39 kDa subunit / NADH:ubiquinone oxidoreductase 49 kD subunit / NADH:ubiquinone oxidoreductase B8 subunit / NADH:ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase subunit 8 / NADH:ubiquinone oxidoreductase 24 kD subunit / NADH dehydrogenase subunit 4L / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c oxidase subunit / cytochrome-c oxidase / Cytochrome c oxidase polypeptide II / Cytochrome c1 / Cytochrome c oxidase subunit 3
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 5.44 Å
AuthorsWaltz, F. / Righetto, R. / Kotecha, A. / Engel, B.D.
Funding support Germany, Switzerland, 2items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: Science / Year: 2025
Title: In-cell architecture of the mitochondrial respiratory chain.
Authors: Florent Waltz / Ricardo D Righetto / Lorenz Lamm / Thalia Salinas-Giegé / Ron Kelley / Xianjun Zhang / Martin Obr / Sagar Khavnekar / Abhay Kotecha / Benjamin D Engel /
Abstract: Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, ...Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome . Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1A: Cytochrome b
1B: Cytochrome b
1C: Cytochrome b-c1 complex subunit Rieske, mitochondrial
1D: Cytochrome b-c1 complex subunit Rieske, mitochondrial
1E: Cytochrome c1
1F: Cytochrome c1
1G: Complex III subunit 9
1H: Complex III subunit 9
1I: Cytochrome b-c1 complex subunit 6
1J: Cytochrome b-c1 complex subunit 6
1K: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
1L: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
1M: MPP-Beta
1N: MPP-Beta
1O: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
1P: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
1Q: Alpha-MPP
1R: Cytochrome b-c1 complex subunit 7
1S: Alpha-MPP
1T: Cytochrome b-c1 complex subunit 7
2A: Cytochrome c oxidase subunit 1
2B: Cytochrome c oxidase polypeptide II
2C: cytochrome-c oxidase
2D: Cytochrome c oxidase subunit 3
2E: Cox5b
2F: Cox5c
2G: Cox6a
2H: Cox6b
2I: Cox7c
2J: Cytochrome c oxidase subunit
2K: Cox7a
2L: CoxIn
3A: Cytochrome c oxidase subunit 1
3B: Cytochrome c oxidase polypeptide II
3C: cytochrome-c oxidase
3D: Cytochrome c oxidase subunit 3
3E: Cox5b
3F: Cox5c
3G: Cox6a
3H: Cox6b
3I: Cox7c
3J: Cytochrome c oxidase subunit
3K: Cox7a
3L: CoxIn
4A: Cytochrome c oxidase subunit 1
4B: Cytochrome c oxidase polypeptide II
4C: cytochrome-c oxidase
4D: Cytochrome c oxidase subunit 3
4E: Cox5b
4F: Cox5c
4G: Cox6a
4H: Cox6b
4I: Cox7c
4J: Cytochrome c oxidase subunit
4K: Cox7a
4L: CoxIn
5A: NADH:ubiquinone oxidoreductase 24 kD subunit
5B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
5C: NADH:ubiquinone oxidoreductase 78 kDa subunit
5D: NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein
5E: NADH:ubiquinone oxidoreductase 49 kD subunit
5F: NADH:ubiquinone oxidoreductase subunit 10
5G: NADH:ubiquinone oxidoreductase subunit 8
5H: B14.5a
5I: Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit
5J: Acyl carrier protein
5K: NADH:ubiquinone oxidoreductase B14 subunit
5L: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
5M: NADH:ubiquinone oxidoreductase 13 kD-like subunit
5N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
5O: NADH:ubiquinone oxidoreductase B8 subunit
5P: Putative NADH:ubiquinone oxidoreductase 39 kDa subunit
5Q: NADH-ubiquinone oxidoreductase chain 1
5R: NADH-ubiquinone oxidoreductase chain 2
5S: NADH-ubiquinone oxidoreductase chain 3
5T: NADH-ubiquinone oxidoreductase chain 4
5U: NADH dehydrogenase subunit 4L
5V: NADH-ubiquinone oxidoreductase chain 5
5W: NADH-ubiquinone oxidoreductase chain 6
5X: ASHI
5Y: P9
5Z: KFYI
5a: AGGG
5b: ESSS
5c: B9
5d: Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit
5e: Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit
5f: Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit
5g: Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit
5h: Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit
5i: NADH:ubiquinone oxidoreductase 15 kDa subunit-like
5j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
5k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
5l: NADH:ubiquinone oxidoreductase 20,9 kD-like subunit
5m: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
5n: Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit
5o: Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit
5p: Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit
5q: Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit
5r: Acyl carrier protein
5s: Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit
5t: CAG2 - CA-like
5u: CAG1
5v: P10
5w: Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit
5x: NUOP8
5y: NUOP7
6A: Cytochrome b
6B: Cytochrome b
6C: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6D: Cytochrome b-c1 complex subunit Rieske, mitochondrial
6E: Cytochrome c1
6F: Cytochrome c1
6G: Complex III subunit 9
6H: Complex III subunit 9
6I: Cytochrome b-c1 complex subunit 6
6J: Cytochrome b-c1 complex subunit 6
6K: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
6L: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8
6M: MPP-Beta
6N: MPP-Beta
6O: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
6P: Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10
6Q: Alpha-MPP
6R: Cytochrome b-c1 complex subunit 7
6S: Alpha-MPP
6T: Cytochrome b-c1 complex subunit 7
7A: Cytochrome c oxidase subunit 1
7B: Cytochrome c oxidase polypeptide II
7C: cytochrome-c oxidase
7D: Cytochrome c oxidase subunit 3
7E: Cox5b
7F: Cox5c
7G: Cox6a
7H: Cox6b
7I: Cox7c
7J: Cytochrome c oxidase subunit
7K: Cox7a
7L: CoxIn
8A: Cytochrome c oxidase subunit 1
8B: Cytochrome c oxidase polypeptide II
8C: cytochrome-c oxidase
8D: Cytochrome c oxidase subunit 3
8E: Cox5b
8F: Cox5c
8G: Cox6a
8H: Cox6b
8I: Cox7c
8J: Cytochrome c oxidase subunit
8K: Cox7a
8L: CoxIn
9A: Cytochrome c oxidase subunit 1
9B: Cytochrome c oxidase polypeptide II
9C: cytochrome-c oxidase
9D: Cytochrome c oxidase subunit 3
9E: Cox5b
9F: Cox5c
9G: Cox6a
9H: Cox6b
9I: Cox7c
9J: Cytochrome c oxidase subunit
9K: Cox7a
9L: CoxIn
A: NADH:ubiquinone oxidoreductase 24 kD subunit
B: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
C: NADH:ubiquinone oxidoreductase 78 kDa subunit
D: NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein
E: NADH:ubiquinone oxidoreductase 49 kD subunit
F: NADH:ubiquinone oxidoreductase subunit 10
G: NADH:ubiquinone oxidoreductase subunit 8
H: B14.5a
I: Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit
J: Acyl carrier protein
K: NADH:ubiquinone oxidoreductase B14 subunit
L: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
M: NADH:ubiquinone oxidoreductase 13 kD-like subunit
N: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
O: NADH:ubiquinone oxidoreductase B8 subunit
P: Putative NADH:ubiquinone oxidoreductase 39 kDa subunit
Q: NADH-ubiquinone oxidoreductase chain 1
R: NADH-ubiquinone oxidoreductase chain 2
S: NADH-ubiquinone oxidoreductase chain 3
T: NADH-ubiquinone oxidoreductase chain 4
U: NADH dehydrogenase subunit 4L
V: NADH-ubiquinone oxidoreductase chain 5
W: NADH-ubiquinone oxidoreductase chain 6
X: ASHI
Y: P9
Z: KFYI
a: AGGG
b: ESSS
c: B9
d: Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit
e: Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit
f: Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit
g: Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit
h: Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit
i: NADH:ubiquinone oxidoreductase 15 kDa subunit-like
j: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
k: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
l: NADH:ubiquinone oxidoreductase 20,9 kD-like subunit
m: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
n: Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit
o: Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit
p: Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit
q: Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit
r: Acyl carrier protein
s: Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit
t: CAG2 - CA-like
u: CAG1
v: P10
w: Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit
x: NUOP8
y: NUOP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,799,956288
Polymers4,769,474214
Non-polymers30,48274
Water00
1


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

-
Components

+
Protein , 27 types, 98 molecules 1A1B6A6B1E1F6E6F1G1H6G6H1M1N6M6N1Q1S6Q6S2C3C4C7C8C9C2E3E4E7E...

#1: Protein
Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42356.465 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P23662
#3: Protein
Cytochrome c1


Mass: 33868.195 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9FQ96, quinol-cytochrome-c reductase
#4: Protein
Complex III subunit 9


Mass: 7040.211 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JC51
#7: Protein
MPP-Beta


Mass: 55121.215 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J5P7
#9: Protein
Alpha-MPP


Mass: 49640.430 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IKI9
#13: Protein
cytochrome-c oxidase / Cytochrome c oxidase polypeptide II


Mass: 17270.035 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9AU02, cytochrome-c oxidase
#15: Protein
Cox5b


Mass: 19051.588 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HRZ4
#16: Protein
Cox5c


Mass: 10886.307 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J7H8
#17: Protein
Cox6a


Mass: 13985.016 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D591
#18: Protein
Cox6b


Mass: 17277.316 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IN92
#19: Protein
Cox7c


Mass: 11356.865 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IU42
#21: Protein
Cox7a


Mass: 6532.420 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D1M1
#22: Protein
CoxIn


Mass: 9905.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JEU7
#30: Protein B14.5a


Mass: 13790.122 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JHV4
#32: Protein
Acyl carrier protein


Mass: 13682.473 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UKY4
#43: Protein NADH dehydrogenase subunit 4L


Mass: 24258.357 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84K56
#46: Protein ASHI


Mass: 17110.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JCW1
#47: Protein P9


Mass: 6764.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DYZ8
#48: Protein KFYI


Mass: 13848.634 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6N0
#49: Protein AGGG


Mass: 14270.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J815
#50: Protein ESSS


Mass: 19630.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J843
#51: Protein B9


Mass: 7334.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IVG9
#55: Protein Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit


Mass: 6497.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QIV8, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#67: Protein CAG2 - CA-like


Mass: 31209.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JFK6
#68: Protein CAG1


Mass: 24319.578 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JHY4
#71: Protein NUOP8


Mass: 17157.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IS53
#72: Protein NUOP7


Mass: 13655.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JA22

+
Cytochrome b-c1 complex subunit ... , 3 types, 12 molecules 1C1D6C6D1I1J6I6J1R1T6R6T

#2: Protein
Cytochrome b-c1 complex subunit Rieske, mitochondrial


Mass: 28545.494 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HEB4, quinol-cytochrome-c reductase
#5: Protein
Cytochrome b-c1 complex subunit 6


Mass: 7991.032 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J8N9
#10: Protein
Cytochrome b-c1 complex subunit 7


Mass: 14062.162 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HX89

+
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit ... , 2 types, 8 molecules 1K1L6K6L1O1P6O6P

#6: Protein
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 8


Mass: 8678.994 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J7I9, quinol-cytochrome-c reductase
#8: Protein
Mitochondrial ubiquinol-cytochrome c oxidoreductase subunit 10


Mass: 6476.588 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J4K5, quinol-cytochrome-c reductase

+
Cytochrome c oxidase ... , 4 types, 24 molecules 2A3A4A7A8A9A2B3B4B7B8B9B2D3D4D7D8D9D2J3J4J7J8J9J

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


Mass: 55194.918 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P08681, cytochrome-c oxidase
#12: Protein
Cytochrome c oxidase polypeptide II


Mass: 30716.742 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9AU05
#14: Protein
Cytochrome c oxidase subunit 3


Mass: 41453.922 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9FV97
#20: Protein
Cytochrome c oxidase subunit


Mass: 11694.374 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8LK22

+
NADH:ubiquinone oxidoreductase ... , 11 types, 22 molecules 5AA5CC5DD5EE5FF5GG5KK5MM5OO5ii5ll

#23: Protein NADH:ubiquinone oxidoreductase 24 kD subunit


Mass: 30643.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9B3, NADH:ubiquinone reductase (H+-translocating)
#25: Protein NADH:ubiquinone oxidoreductase 78 kDa subunit


Mass: 78432.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UKY6, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#26: Protein NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein


Mass: 32178.600 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IHL3
#27: Protein NADH:ubiquinone oxidoreductase 49 kD subunit


Mass: 52672.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9A8, NADH:ubiquinone reductase (H+-translocating)
#28: Protein NADH:ubiquinone oxidoreductase subunit 10


Mass: 18144.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9B0, NADH:ubiquinone reductase (H+-translocating)
#29: Protein NADH:ubiquinone oxidoreductase subunit 8


Mass: 26530.150 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9B1, NADH:ubiquinone reductase (H+-translocating)
#33: Protein NADH:ubiquinone oxidoreductase B14 subunit


Mass: 16135.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UKY9, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#35: Protein NADH:ubiquinone oxidoreductase 13 kD-like subunit


Mass: 16306.489 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UP30, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#37: Protein NADH:ubiquinone oxidoreductase B8 subunit


Mass: 11012.532 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9A9, NADH:ubiquinone reductase (H+-translocating)
#57: Protein NADH:ubiquinone oxidoreductase 15 kDa subunit-like


Mass: 9565.950 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6TH88, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#60: Protein NADH:ubiquinone oxidoreductase 20,9 kD-like subunit


Mass: 13461.300 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UP28, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

+
NADH dehydrogenase [ubiquinone] ... , 6 types, 12 molecules 5BB5LL5NN5jj5kk5mm

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


Mass: 52303.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A8ICJ1, NADH:ubiquinone reductase (H+-translocating)
#34: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 20648.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UP29
#36: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 18034.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UP31
#58: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7


Mass: 10295.870 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UKY7
#59: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Complex I-B22 / NADH-ubiquinone oxidoreductase B22 subunit


Mass: 13951.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UKY8
#61: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13


Mass: 16400.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UP32

+
Mitochondrial NADH:ubiquinone oxidoreductase ... , 9 types, 18 molecules 5II5dd5ee5ff5hh5pp5qq5ss5ww

#31: Protein Mitochondrial NADH:ubiquinone oxidoreductase 18 kDa subunit


Mass: 17977.553 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UKY3, NADH:ubiquinone reductase (H+-translocating)
#52: Protein Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit


Mass: 9994.435 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY2, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#53: Protein Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit


Mass: 23390.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY4, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#54: Protein Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit


Mass: 7651.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QIV4, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#56: Protein Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit


Mass: 16187.231 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QIV9, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#64: Protein Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit


Mass: 15291.994 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY0, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#65: Protein Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit


Mass: 22349.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY1, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#66: Protein Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit / Putative gamma carbonic anhydrase


Mass: 32729.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6S7R7, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#70: Protein Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit


Mass: 12159.065 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY5, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

+
Putative NADH:ubiquinone oxidoreductase ... , 3 types, 6 molecules 5PP5nn5oo

#38: Protein Putative NADH:ubiquinone oxidoreductase 39 kDa subunit


Mass: 43709.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V506
#62: Protein Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit


Mass: 12542.351 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V504
#63: Protein Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit


Mass: 17907.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V505

+
NADH-ubiquinone oxidoreductase chain ... , 6 types, 12 molecules 5QQ5RR5SS5TT5VV5WW

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


Mass: 31606.412 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P11658, NADH:ubiquinone reductase (H+-translocating)
#40: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 42834.082 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: Extension in N-ter not present in UNIPROT entry,Extension in N-ter not present in UNIPROT entry
Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P08740, NADH:ubiquinone reductase (H+-translocating)
#41: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 30207.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V502
#42: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 48766.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P20113, NADH:ubiquinone reductase (H+-translocating)
#44: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 59087.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P08739, NADH:ubiquinone reductase (H+-translocating)
#45: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 17756.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P10329, NADH:ubiquinone reductase (H+-translocating)

+
Protein/peptide , 1 types, 2 molecules 5vv

#69: Protein/peptide P10


Mass: 5122.813 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Frame shifted version of CHLRE_08g368050v5 / Source: (natural) Chlamydomonas reinhardtii (plant)

+
Non-polymers , 13 types, 74 molecules

#73: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#74: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#75: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#76: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#77: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#78: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#79: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu2
#80: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#81: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#82: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#83: Chemical
ChemComp-8Q1 / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate / S-dodecanoyl-4'-phosphopantetheine


Mass: 540.651 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#84: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#85: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O17P3S

+
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Chlamydomonas reinhardtii / Type: CELL / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 143.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
1STOPGAP0.7.1volume selection
2PyTom0.5.0volume selection
3FEI tomography5image acquisition
5RELION4CTF correction
12RELION4final Euler assignment
13RELION4classification
14RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 5.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14488 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Template Matching / Num. of tomograms: 131 / Num. of volumes extracted: 26591

+
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