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- PDB-9f5y: Structure of the Chlamydomonas reinhardtii respiratory complex I ... -

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Basic information

Entry
Database: PDB / ID: 9f5y
TitleStructure of the Chlamydomonas reinhardtii respiratory complex I from respiratory supercomplex
Components
  • (Mitochondrial NADH:ubiquinone oxidoreductase ...) x 9
  • (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
  • B14.5a
  • B9
  • CAG1
  • CAG2 - CA-like
  • ESSS
  • KFYI
  • Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit
  • NADH dehydrogenase subunit 4L
  • NUOP7
  • NUOP8
  • P10
  • P9
KeywordsMEMBRANE PROTEIN / Mitochondria / respiratory complex / respiration / alga
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / TIM22 mitochondrial import inner membrane insertion complex / NADH dehydrogenase / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / ubiquinone biosynthetic process / oxidoreductase activity, acting on NAD(P)H / acyl binding / acyl carrier activity ...NADH:ubiquinone reductase (H+-translocating) / TIM22 mitochondrial import inner membrane insertion complex / NADH dehydrogenase / mitochondrion targeting sequence binding / protein insertion into mitochondrial inner membrane / NADH dehydrogenase complex / ubiquinone biosynthetic process / oxidoreductase activity, acting on NAD(P)H / acyl binding / acyl carrier activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / phosphopantetheine binding / protein transmembrane transporter activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron 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 / mitochondrial inner membrane / oxidoreductase activity / protein-containing complex binding / mitochondrion / metal ion binding / membrane
Similarity search - Function
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 / Hexapeptide repeat / Tim17/Tim22/Tim23/Pmp24 family / Bacterial transferase hexapeptide (six repeats) ...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 / Hexapeptide repeat / Tim17/Tim22/Tim23/Pmp24 family / Bacterial transferase hexapeptide (six repeats) / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / 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 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / Trimeric LpxA-like superfamily / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / SLBB domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like
Similarity search - Domain/homology
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Chem-8Q1 / CARDIOLIPIN / CROTONYL COENZYME A / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PC7 / Chem-PGT / PHOSPHATIDYLETHANOLAMINE ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Chem-8Q1 / CARDIOLIPIN / CROTONYL COENZYME A / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / Chem-PC7 / Chem-PGT / PHOSPHATIDYLETHANOLAMINE / IRON/SULFUR CLUSTER / Chem-UQ5 / Uncharacterized protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / 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 / 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
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.51 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Apr 2, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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)1,181,719105
Polymers1,141,13151
Non-polymers40,58854
Water32,9131827
1


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

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Components

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NADH:ubiquinone oxidoreductase ... , 11 types, 11 molecules ACDEFGKMOil

#1: Protein NADH:ubiquinone oxidoreductase 24 kD subunit


Mass: 30643.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9B3, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH:ubiquinone oxidoreductase 78 kDa subunit


Mass: 78432.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UKY6, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#4: Protein NADH:ubiquinone oxidoreductase 30kDa subunit domain-containing protein


Mass: 32178.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IHL3
#5: Protein NADH:ubiquinone oxidoreductase 49 kD subunit


Mass: 52672.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9A8, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH:ubiquinone oxidoreductase subunit 10


Mass: 18144.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9B0, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH:ubiquinone oxidoreductase subunit 8


Mass: 26530.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9B1, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH:ubiquinone oxidoreductase B14 subunit


Mass: 16135.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UKY9, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#13: Protein NADH:ubiquinone oxidoreductase 13 kD-like subunit


Mass: 16306.489 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UP30, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#15: Protein NADH:ubiquinone oxidoreductase B8 subunit


Mass: 11012.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6V9A9, NADH:ubiquinone reductase (H+-translocating)
#35: Protein NADH:ubiquinone oxidoreductase 15 kDa subunit-like


Mass: 9565.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6TH88, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#38: Protein NADH:ubiquinone oxidoreductase 20,9 kD-like subunit


Mass: 13461.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UP28, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

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NADH dehydrogenase [ubiquinone] ... , 6 types, 6 molecules BLNjkm

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


Mass: 52303.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A8ICJ1, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


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


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


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


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


Mass: 16400.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UP32

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Protein , 14 types, 15 molecules HJrUXYZabcgtuxy

#8: Protein B14.5a


Mass: 13790.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JHV4
#10: Protein Acyl carrier protein


Mass: 13682.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6UKY4
#21: Protein NADH dehydrogenase subunit 4L


Mass: 24258.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q84K56
#24: Protein ASHI


Mass: 17110.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JCW1
#25: Protein P9


Mass: 6764.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DYZ8
#26: Protein KFYI


Mass: 13848.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J6N0
#27: Protein AGGG


Mass: 14270.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J815
#28: Protein ESSS


Mass: 19630.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J843
#29: Protein B9


Mass: 7334.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IVG9
#33: Protein Mitochondrial putative NADH:ubiquinone oxidoreductase 6.5 kDa subunit


Mass: 6497.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QIV8, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#45: Protein CAG2 - CA-like


Mass: 31209.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JFK6
#46: Protein CAG1


Mass: 24319.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JHY4
#49: Protein NUOP8


Mass: 17157.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IS53
#50: Protein NUOP7


Mass: 13655.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JA22

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Mitochondrial NADH:ubiquinone oxidoreductase ... , 9 types, 9 molecules Idefhpqsw

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


Mass: 17977.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6UKY3, NADH:ubiquinone reductase (H+-translocating)
#30: Protein Mitochondrial NADH:ubiquinone oxidoreductase 10 kDa subunit


Mass: 9994.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY2, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#31: Protein Mitochondrial NADH:ubiquinone oxidoreductase 23 kDa subunit


Mass: 23390.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY4, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#32: Protein Mitochondrial NADH:ubiquinone oxidoreductase 7.5 kDa subunit


Mass: 7651.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QIV4, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#34: Protein Mitochondrial NADH:ubiquinone oxidoreductase 13 kDa subunit


Mass: 16187.231 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QIV9, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#42: Protein Mitochondrial NADH:ubiquinone oxidoreductase 16 kDa subunit


Mass: 15291.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY0, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#43: Protein Mitochondrial NADH:ubiquinone oxidoreductase 19 kDa subunit


Mass: 22349.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY1, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#44: Protein Mitochondrial NADH:ubiquinone oxidoreductase 32 kDa subunit / Putative gamma carbonic anhydrase


Mass: 32729.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6S7R7, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#48: Protein Mitochondrial NADH:ubiquinone oxidoreductase 9 kDa subunit


Mass: 12159.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: Q6QAY5, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase

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Putative NADH:ubiquinone oxidoreductase ... , 3 types, 3 molecules Pno

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


Mass: 43709.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V506
#40: Protein Putative NADH:ubiquinone oxidoreductase 12.5 kDa subunit


Mass: 12542.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V504
#41: Protein Putative NADH:ubiquinone oxidoreductase 17.8 kDa subunit


Mass: 17907.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V505

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NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules QRSTVW

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


Mass: 31606.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P11658, NADH:ubiquinone reductase (H+-translocating)
#18: Protein NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase subunit 2


Mass: 42763.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Extension in N-ter visible in the structure, but not in UNIPROT,Extension in N-ter visible in the structure, but not in UNIPROT
Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P08740, NADH:ubiquinone reductase (H+-translocating)
#19: Protein NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase subunit 3


Mass: 30207.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q6V502
#20: Protein NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase subunit 4


Mass: 48766.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P20113, NADH:ubiquinone reductase (H+-translocating)
#22: Protein NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase subunit 5


Mass: 59087.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P08739, NADH:ubiquinone reductase (H+-translocating)
#23: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 17756.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P10329, NADH:ubiquinone reductase (H+-translocating)

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Protein/peptide , 1 types, 1 molecules v

#47: Protein/peptide P10


Mass: 5122.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Frame shifted version of Chlre_08g368050v5, not in UNIPROT
Source: (natural) Chlamydomonas reinhardtii (plant)

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Non-polymers , 14 types, 1881 molecules

#51: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#53: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#54: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#55: 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.: 2 / Source method: obtained synthetically / Formula: C23H45N2O8PS
#56: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#57: Chemical ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50O4
#58: Chemical
ChemComp-PC7 / (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / PHOSPHATIDYLCHOLINE / 1-PALMITOYL-2-STEAROYL-PC


Mass: 763.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H85NO8P / Comment: phospholipid*YM
#59: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C39H77O8P
#60: 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.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#61: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#62: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O17P3S
#63: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#64: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1827 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Chlamydomonas reinhardtii respirasome / Type: COMPLEX / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83443 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006139259
ELECTRON MICROSCOPYf_angle_d0.865188735
ELECTRON MICROSCOPYf_dihedral_angle_d10.39120602
ELECTRON MICROSCOPYf_chiral_restr0.05320306
ELECTRON MICROSCOPYf_plane_restr0.00723689

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