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- PDB-8e73: Vigna radiata supercomplex I+III2 (full bridge) -

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Basic information

Entry
Database: PDB / ID: 8.0E+73
TitleVigna radiata supercomplex I+III2 (full bridge)
Components
  • (MPP-alpha (protomer ...) x 2
  • COB (cyt b)
  • CYC1 (cyt c1)
  • MPP-beta
  • NDUA1
  • NDUA11
  • NDUA12
  • NDUA13
  • NDUA2
  • NDUA3
  • NDUA5
  • NDUA6
  • NDUA7
  • NDUA8
  • NDUA9
  • NDUAB1-alpha
  • NDUAB1-beta
  • NDUB10
  • NDUB11
  • NDUB2
  • NDUB3
  • NDUB4
  • NDUB6
  • NDUB7
  • NDUB8
  • NDUB9
  • NDUC2
  • NDUCA1
  • NDUCA2
  • NDUCAL2
  • NDUFX
  • NDUP1
  • NDUP2
  • NDUP4
  • NDUS1
  • NDUS2
  • NDUS3
  • NDUS4
  • NDUS5
  • NDUS6
  • NDUS7
  • NDUS8
  • NDUV1
  • NDUV2
  • NDUX1
  • Nad1
  • Nad2
  • Nad3
  • Nad4
  • Nad4L
  • Nad5
  • Nad6
  • QCR10 (UCRY)
  • QCR6
  • QCR7
  • QCR8
  • QCR9
  • UCR1 (Rieske iron-sulfur protein subunit)
KeywordsELECTRON TRANSPORT / respiratory supercomplex / nadh-cyt c oxidoreductase / membrane complex
Function / homology
Function and homology information


TIM22 mitochondrial import inner membrane insertion complex / mitochondrion targeting sequence binding / P450-containing electron transport chain / : / protein insertion into mitochondrial inner membrane / : / NADH dehydrogenase complex / thylakoid / : / respiratory chain complex III ...TIM22 mitochondrial import inner membrane insertion complex / mitochondrion targeting sequence binding / P450-containing electron transport chain / : / protein insertion into mitochondrial inner membrane / : / NADH dehydrogenase complex / thylakoid / : / respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / acyl binding / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / protein transmembrane transporter activity / electron transport coupled proton transport / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / respiratory chain complex I / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / chloroplast / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / 4 iron, 4 sulfur cluster binding / response to oxidative stress / electron transfer activity / mitochondrial inner membrane / mRNA binding / heme binding / protein-containing complex binding / mitochondrion / proteolysis / membrane / nucleus / metal ion binding / cytoplasm
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 dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / At2g27730-like / : / : ...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 dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / At2g27730-like / : / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Hexapeptide repeat of succinyl-transferase / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / : / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Hexapeptide repeat / Cytochrome c1 / Cytochrome C1 family / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / 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) / Zinc finger, CHCC-type / Zinc-finger domain / Metalloenzyme, LuxS/M16 peptidase-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / 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 / NDUFA6, LYR domain / 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 / Trimeric LpxA-like superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / 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 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / : / Complex 1 protein (LYR family) / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / 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 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NAD-dependent epimerase/dehydratase
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / : / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / : / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / UBIQUINONE-10 / Chem-ZMP / Acyl carrier protein / NADH dehydrogenase [ubiquinone] flavoprotein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein LOC106754061 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / Outer envelope pore protein 16-3, chloroplastic/mitochondrial / Serine/arginine-rich-splicing factor SR34 isoform X2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / Complex III subunit 9 / Uncharacterized protein LOC106758628 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Probable mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Uncharacterized protein LOC106761134 / Gamma carbonic anhydrase 1, mitochondrial-like / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Mitochondrial-processing peptidase subunit alpha / Gamma carbonic anhydrase-like 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Uncharacterized protein LOC106766640 / Uncharacterized protein LOC106767179 / Uncharacterized protein LOC106768957 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / Uncharacterized protein LOC106771273 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1 / Mitochondrial-processing peptidase subunit alpha / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / Cytochrome b-c1 complex subunit 6 / Uncharacterized protein LOC106775330 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / Uncharacterized protein LOC106779486 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Cytochrome c1-2, heme protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH-ubiquinone oxidoreductase chain 3
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMaldonado, M. / Letts, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0022293 United States
CitationJournal: Nat Plants / Year: 2023
Title: Plant-specific features of respiratory supercomplex I + III from Vigna radiata.
Authors: M Maldonado / Z Fan / K M Abe / J A Letts /
Abstract: The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane ...The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.
History
DepositionAug 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPP-beta
B: MPP-alpha (protomer 1)
C: COB (cyt b)
D: CYC1 (cyt c1)
E: UCR1 (Rieske iron-sulfur protein subunit)
F: QCR7
G: QCR8
H: QCR6
J: QCR9
K: QCR10 (UCRY)
M: MPP-beta
N: MPP-alpha (protomer 2)
O: COB (cyt b)
P: CYC1 (cyt c1)
Q: UCR1 (Rieske iron-sulfur protein subunit)
R: QCR7
S: QCR8
T: QCR6
V: QCR9
W: QCR10 (UCRY)
1M: Nad1
2M: Nad2
3M: Nad3
4M: Nad4
4L: Nad4L
5M: Nad5
6M: Nad6
A1: NDUA1
A2: NDUA2
A3: NDUA3
A5: NDUA5
A6: NDUA6
A7: NDUA7
A8: NDUA8
A9: NDUA9
AK: NDUA11
AL: NDUA12
AM: NDUA13
AC: NDUAB1-beta
AB: NDUAB1-alpha
B2: NDUB2
B3: NDUB3
B4: NDUB4
B7: NDUB7
B8: NDUB8
B9: NDUB9
BJ: NDUB10
BK: NDUB11
FD: NDUFX
C2: NDUC2
P2: NDUP2
G1: NDUCA1
G2: NDUCA2
L2: NDUCAL2
S1: NDUS1
S2: NDUS2
S3: NDUS3
S4: NDUS4
S5: NDUS5
S6: NDUS6
S7: NDUS7
S8: NDUS8
P1: NDUP1
P4: NDUP4
C1: NDUB6
V1: NDUV1
V2: NDUV2
X1: NDUX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,622,406114
Polymers1,588,83568
Non-polymers33,57246
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 57 types, 66 molecules AMCODPEQFRGSHTJVKW1M2M3M4M4L5M6MA1A2A3A5A6...

#1: Protein MPP-beta


Mass: 58711.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TWG4
#3: Protein COB (cyt b)


Mass: 44454.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#4: Protein CYC1 (cyt c1)


Mass: 33556.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3W199
#5: Protein UCR1 (Rieske iron-sulfur protein subunit)


Mass: 30051.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
References: UniProt: A0A1S3TB49, quinol-cytochrome-c reductase
#6: Protein QCR7


Mass: 14392.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U9J1
#7: Protein QCR8


Mass: 8349.831 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U9S5
#8: Protein QCR6


Mass: 8117.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VHC0
#9: Protein QCR9


Mass: 8203.420 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQD2
#10: Protein QCR10 (UCRY)


Mass: 8948.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#12: Protein Nad1


Mass: 35771.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#13: Protein Nad2


Mass: 54063.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#14: Protein Nad3


Mass: 13746.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: G9JLR0
#15: Protein Nad4


Mass: 55823.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#16: Protein Nad4L


Mass: 11153.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#17: Protein Nad5


Mass: 74895.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#18: Protein Nad6


Mass: 23604.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#19: Protein NDUA1


Mass: 7357.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TU57
#20: Protein NDUA2


Mass: 10884.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TVC7
#21: Protein NDUA3


Mass: 6695.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TCK0
#22: Protein NDUA5


Mass: 18977.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U023
#23: Protein NDUA6


Mass: 14920.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3W1K8
#24: Protein NDUA7


Mass: 14356.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UVC7
#25: Protein NDUA8


Mass: 12022.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VVN6
#26: Protein NDUA9


Mass: 43781.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3V8W7
#27: Protein NDUA11


Mass: 17284.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TLY8
#28: Protein NDUA12


Mass: 18192.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VNK7
#29: Protein NDUA13


Mass: 16189.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UYW0
#30: Protein NDUAB1-beta


Mass: 13066.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A0L9U2J6
#31: Protein NDUAB1-alpha


Mass: 14314.356 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VXS7
#32: Protein NDUB2


Mass: 7555.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TFG6
#33: Protein NDUB3


Mass: 7843.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UVV0
#34: Protein NDUB4


Mass: 8364.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3ULL3
#35: Protein NDUB7


Mass: 11600.554 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3V2B8
#36: Protein NDUB8


Mass: 13592.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UJ95
#37: Protein NDUB9


Mass: 13519.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U1J6
#38: Protein NDUB10


Mass: 12587.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VGT1
#39: Protein NDUB11


Mass: 13157.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3V2Z3
#40: Protein NDUFX


Mass: 17610.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VXN7
#41: Protein NDUC2


Mass: 9243.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#42: Protein NDUP2


Mass: 12172.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A0L9V7A4
#43: Protein NDUCA1


Mass: 29333.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VT00
#44: Protein NDUCA2


Mass: 29780.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U544
#45: Protein NDUCAL2


Mass: 28268.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UI49
#46: Protein NDUS1


Mass: 81434.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQ85
#47: Protein NDUS2


Mass: 45031.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#48: Protein NDUS3


Mass: 22926.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#49: Protein NDUS4


Mass: 16435.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UIW7
#50: Protein NDUS5


Mass: 9966.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQ33
#51: Protein NDUS6


Mass: 11582.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VYF3
#52: Protein NDUS7


Mass: 23710.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U8J5
#53: Protein NDUS8


Mass: 25545.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A0L9VFH0
#54: Protein NDUP1


Mass: 11245.803 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U2B9
#55: Protein NDUP4


Mass: 7316.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UND4
#56: Protein NDUB6


Mass: 9708.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TTD7
#57: Protein NDUV1


Mass: 53904.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#58: Protein NDUV2


Mass: 27992.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A0L9UNZ4
#59: Protein NDUX1


Mass: 10949.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VI15

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MPP-alpha (protomer ... , 2 types, 2 molecules BN

#2: Protein MPP-alpha (protomer 1)


Mass: 55244.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3UHF9
#11: Protein MPP-alpha (protomer 2)


Mass: 54537.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VF71

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Non-polymers , 13 types, 46 molecules

#60: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#61: 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
#62: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#63: 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.: 8 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#64: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#65: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#66: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#67: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#68: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#69: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#70: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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


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

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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: Vigna radiata supercomplex I+III2 (full bridge) / Type: COMPLEX
Details: Higher-order assembly between respiratory complex I and complex III2
Entity ID: #1-#59 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vigna radiata (mung bean)
Buffer solutionpH: 7.7
Details: 0.2% digitonin, 30 mM HEPES pH 7.7, 150 mM potassium acetate, 1 mM EDTA, 0.002% PMSF
SpecimenConc.: 1.55 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Digitonin-extracted, amphipol (A8-35)stabilized
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Details: 4 ul, 20 seconds pre-blot, blot 4 seconds

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 25712

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123451 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003100136
ELECTRON MICROSCOPYf_angle_d0.544135727
ELECTRON MICROSCOPYf_dihedral_angle_d8.06214503
ELECTRON MICROSCOPYf_chiral_restr0.04214886
ELECTRON MICROSCOPYf_plane_restr0.00417155

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