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- PDB-9g9y: Respiratory supercomplex CI2-CIII2-CIV2 (megacomplex) from alphap... -

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Basic information

Entry
Database: PDB / ID: 9g9y
TitleRespiratory supercomplex CI2-CIII2-CIV2 (megacomplex) from alphaproteobacterium
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • (NADH dehydrogenase subunit ...) x 3
  • (NADH-quinone oxidoreductase subunit ...) x 10
  • Aa3 type cytochrome c oxidase subunit IV
  • Cytochrome b
  • Cytochrome c, class I
  • Cytochrome c1
  • ETC complex I subunit conserved region
  • NAD-dependent epimerase/dehydratase
  • NADH-quinone oxidoreductase
  • NADH:ubiquinone oxidoreductase 17.2 kD subunit
  • Protein-L-isoaspartate O-methyltransferase
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
  • Zinc finger CHCC-type domain-containing protein
  • cytochrome-c oxidase
KeywordsELECTRON TRANSPORT / Supercomplex / multi-subunit membrane protein complex / electron transport chain / native purification
Function / homology
Function and homology information


active transmembrane transporter activity / organelle envelope / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / NADH:ubiquinone reductase (H+-translocating) / : / membrane protein complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / aerobic electron transport chain ...active transmembrane transporter activity / organelle envelope / protein-L-isoaspartate (D-aspartate) O-methyltransferase activity / NADH:ubiquinone reductase (H+-translocating) / : / membrane protein complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / aerobic electron transport chain / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / monoatomic cation transmembrane transporter activity / oxidative phosphorylation / quinol-cytochrome-c reductase / : / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / NADH dehydrogenase activity / organelle membrane / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / catalytic complex / quinone binding / ATP synthesis coupled electron transport / endomembrane system / aerobic respiration / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / methylation / oxidoreductase activity / electron transfer activity / iron ion binding / copper ion binding / heme binding / protein-containing complex binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Protein-L-isoaspartate(D-aspartate) O-methyltransferase / Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) / Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Cytochrome c oxidase, subunit I bacterial type / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase, subunit II / Cytochrome c, class IA/ IB / 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 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 c/quinol oxidase subunit II / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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 c1 / Cytochrome C1 family / 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. / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / 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 / Cytochrome c / 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-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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 / Rieske [2Fe-2S] domain / NADH-quinone oxidoreductase, chain 5-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / Rieske [2Fe-2S] iron-sulphur domain superfamily / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH dehydrogenase, subunit C
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-DU0 / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C ...1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / COPPER (II) ION / DINUCLEAR COPPER ION / Chem-DU0 / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME-A / HEME C / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-P5S / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / Aa3 type cytochrome c oxidase subunit IV / NAD-dependent epimerase/dehydratase / NADH:ubiquinone oxidoreductase 17.2 kD subunit / ETC complex I subunit conserved region / Cytochrome c, class I / Zinc finger CHCC-type domain-containing protein / Cytochrome c oxidase subunit 1 / NADH-quinone oxidoreductase subunit N / NADH dehydrogenase subunit M / NADH dehydrogenase subunit L / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase / NADH-quinone oxidoreductase subunit F / NADH dehydrogenase subunit E / NADH-quinone oxidoreductase subunit D / NADH-quinone oxidoreductase subunit C / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit A / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome b / Cytochrome c1 / Protein-L-isoaspartate O-methyltransferase / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesParacoccus denitrificans PD1222 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.91 Å
AuthorsYaikhomba, M. / Hirst, J. / Croll, T.I. / Spikes, T.E. / Agip, A.N.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 and MC_UU_00028/1 United Kingdom
CitationJournal: To Be Published
Title: Minimal supercomplexes in alphaproteobacteria reveal conserved structural mechanisms for efficient respiration
Authors: Yaikhomba, M. / Hirst, J. / Croll, T.I. / Spikes, T.E.
History
DepositionJul 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH-quinone oxidoreductase subunit A
A1: NADH-quinone oxidoreductase subunit A
B: NADH-quinone oxidoreductase subunit B
B1: NADH-quinone oxidoreductase subunit B
C: NADH-quinone oxidoreductase subunit C
C1: NADH-quinone oxidoreductase subunit C
D: NADH-quinone oxidoreductase subunit D
D1: NADH-quinone oxidoreductase subunit D
E: NADH dehydrogenase subunit E
E1: NADH dehydrogenase subunit E
F: NADH-quinone oxidoreductase subunit F
F1: NADH-quinone oxidoreductase subunit F
G: NADH-quinone oxidoreductase
G1: NADH-quinone oxidoreductase
H: NADH-quinone oxidoreductase subunit H
H1: NADH-quinone oxidoreductase subunit H
I: NADH-quinone oxidoreductase subunit I
I1: NADH-quinone oxidoreductase subunit I
J: NADH-quinone oxidoreductase subunit J
J1: NADH-quinone oxidoreductase subunit J
K: NADH-quinone oxidoreductase subunit K
K1: NADH-quinone oxidoreductase subunit K
L: NADH dehydrogenase subunit L
L1: NADH dehydrogenase subunit L
M: NADH dehydrogenase subunit M
M1: NADH dehydrogenase subunit M
N: NADH-quinone oxidoreductase subunit N
N1: NADH-quinone oxidoreductase subunit N
P: NAD-dependent epimerase/dehydratase
P1: NAD-dependent epimerase/dehydratase
Q: ETC complex I subunit conserved region
Q1: ETC complex I subunit conserved region
R: Zinc finger CHCC-type domain-containing protein
R1: Zinc finger CHCC-type domain-containing protein
Z: Protein-L-isoaspartate O-methyltransferase
Z1: Protein-L-isoaspartate O-methyltransferase
a: Cytochrome b
b: Cytochrome c1
c: Ubiquinol-cytochrome c reductase iron-sulfur subunit
d: Cytochrome b
e: Cytochrome c1
f: Ubiquinol-cytochrome c reductase iron-sulfur subunit
g: Cytochrome c oxidase subunit 1
h: Cytochrome c oxidase subunit 2
i: cytochrome-c oxidase
j: Aa3 type cytochrome c oxidase subunit IV
k: Cytochrome c oxidase subunit 1
l: Cytochrome c oxidase subunit 2
m: cytochrome-c oxidase
n: Aa3 type cytochrome c oxidase subunit IV
o: Cytochrome c, class I
p: Cytochrome c, class I
q: NADH:ubiquinone oxidoreductase 17.2 kD subunit
q1: NADH:ubiquinone oxidoreductase 17.2 kD subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,825,249141
Polymers1,779,69854
Non-polymers45,55187
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration, native gel electrophoresis, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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NADH-quinone oxidoreductase subunit ... , 10 types, 20 molecules AA1BB1CC1DD1FF1HH1II1JJ1KK1NN1

#1: Protein NADH-quinone oxidoreductase subunit A


Mass: 13686.093 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B498
#2: Protein NADH-quinone oxidoreductase subunit B


Mass: 19525.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B497
#3: Protein NADH-quinone oxidoreductase subunit C


Mass: 23920.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B496
#4: Protein NADH-quinone oxidoreductase subunit D


Mass: 46811.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B495
#6: Protein NADH-quinone oxidoreductase subunit F


Mass: 47281.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B491
#8: Protein NADH-quinone oxidoreductase subunit H


Mass: 38861.152 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B487
#9: Protein NADH-quinone oxidoreductase subunit I


Mass: 18925.561 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B486
#10: Protein NADH-quinone oxidoreductase subunit J


Mass: 21732.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B483, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#11: Protein NADH-quinone oxidoreductase subunit K / NADH dehydrogenase I subunit K / NADH dehydrogenase I / subunit 11 / NADH-quinone oxidoreductase ...NADH dehydrogenase I subunit K / NADH dehydrogenase I / subunit 11 / NADH-quinone oxidoreductase subunit 11 / NQO11 / NDH-1 subunit K / NDH-1


Mass: 10863.054 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B482, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#14: Protein NADH-quinone oxidoreductase subunit N


Mass: 52564.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B479

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NADH dehydrogenase subunit ... , 3 types, 6 molecules EE1LL1MM1

#5: Protein NADH dehydrogenase subunit E


Mass: 26145.865 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B494
#12: Protein NADH dehydrogenase subunit L


Mass: 77839.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B481, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH dehydrogenase subunit M


Mass: 56547.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B480, NADH:ubiquinone reductase (H+-translocating)

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Protein , 12 types, 24 molecules GG1PP1QQ1RR1ZZ1adbecfimjnopqq1

#7: Protein NADH-quinone oxidoreductase


Mass: 73289.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B489, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#15: Protein NAD-dependent epimerase/dehydratase


Mass: 35386.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1AZB0
#16: Protein ETC complex I subunit conserved region


Mass: 12048.399 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B1M0
#17: Protein Zinc finger CHCC-type domain-containing protein


Mass: 7069.931 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B357
#18: Protein Protein-L-isoaspartate O-methyltransferase


Mass: 23528.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B5L6
#19: Protein Cytochrome b


Mass: 50154.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B4F3
#20: Protein Cytochrome c1


Mass: 46904.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B4F4
#21: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 20889.236 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B4F2, quinol-cytochrome-c reductase
#24: Protein cytochrome-c oxidase / Cytochrome aa3 subunit 3 / Cytochrome c oxidase polypeptide III


Mass: 30833.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1BA37, cytochrome-c oxidase
#25: Protein Aa3 type cytochrome c oxidase subunit IV


Mass: 7351.497 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1AZ52
#26: Protein Cytochrome c, class I


Mass: 18177.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B311
#27: Protein NADH:ubiquinone oxidoreductase 17.2 kD subunit


Mass: 14460.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B1H8

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Cytochrome c oxidase subunit ... , 2 types, 4 molecules gkhl

#22: Protein Cytochrome c oxidase subunit 1


Mass: 62486.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1B3D7, cytochrome-c oxidase
#23: Protein Cytochrome c oxidase subunit 2


Mass: 32563.643 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Paracoccus denitrificans PD1222 (bacteria)
References: UniProt: A1BA41, cytochrome-c oxidase

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Non-polymers , 18 types, 87 molecules

#28: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical
ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C59H90O4
#30: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#31: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#32: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#33: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#34: Chemical
ChemComp-DU0 / 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol


Mass: 516.752 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H52O5
#35: 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.: 9 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#36: Chemical
ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H77O8P
#37: Chemical ChemComp-P5S / O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine / phosphatidyl serine


Mass: 792.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO10P
#38: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#39: 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
#40: 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.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#41: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#42: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#43: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#44: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#45: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2

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Details

Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Respiratory supercomplex CI2-CIII2-CIV2 from alphaproteobacteriumCOMPLEX#1-#270NATURAL
2Alphaproteobacterial respiratory complex I (NADH-ubiquinone oxidoreductase)COMPLEX#1-#18, #271NATURAL
3Alphaproteobacterial respiratory complex III (ubiquinone-cytochrome c oxidoreductase, cytochrome bc1)COMPLEX#19-#211NATURAL
4Alphaproteobacterial respiratory complex IV (Cytochrome c oxidase, aa3-type)COMPLEX#22-#251NATURAL
5Transmembrane-anchored cytochrome c (c552)COMPLEX#261NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Paracoccus denitrificans PD1222 (bacteria)318586
33Paracoccus denitrificans PD1222 (bacteria)318586
44Paracoccus denitrificans PD1222 (bacteria)318586
55Paracoccus denitrificans PD1222 (bacteria)318586
Buffer solutionpH: 7.5
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 55.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3002 / Symmetry type: POINT

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