[English] 日本語
Yorodumi
- PDB-8b6f: Cryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b6f
TitleCryo-EM structure of NADH:ubiquinone oxidoreductase (complex-I) from respiratory supercomplex of Tetrahymena thermophila
Components
  • (Acyl carrier ...) x 2
  • (Gamma-carbonic ...) x 2
  • (NADH dehydrogenase [ubiquinone] ...) x 6
  • (NADH dehydrogenase subunit ...) x 5
  • (NADH-ubiquinone oxidoreductase ...) x 7
  • (Transmembrane protein, ...) x 11
  • 2 iron, 2 sulfur cluster-binding protein
  • 37S ribosomal protein S25, mitochondrial
  • ATP synthase subunit e, mitochondrial
  • Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
  • CHCH domain-containing protein
  • COX assembly mitochondrial protein
  • CX9C domain-containing protein
  • Complex I-MNLL
  • DnaJ domain protein
  • ETC complex I subunit motif protein
  • GRAM domain protein
  • Lipid-A-disaccharide synthase
  • NAD-dependent epimerase/dehydratase family protein
  • NADH dehydrogenase, putative
  • ND1b
  • NDUA13
  • NDUB10
  • NDUB15
  • NDUB4
  • NDUB6
  • NDUB8
  • NDUPH2
  • NDUTT15
  • NDUTT16
  • NDUTT17
  • PH domain-containing protein
  • RNase III domain-containing protein
  • Ribosomal protein L51/S25/CI-B8 domain protein
  • Thioredoxin
  • Transcription factor apfi protein, putative
  • Transmembrane protein
  • Ymf57
  • Ymf58
  • Ymf62
  • Ymf65
  • Zinc-finger protein
KeywordsELECTRON TRANSPORT / Ciliate / mitochondrial / complex-I / supercomplex
Function / homology
Function and homology information


lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / NADH:ubiquinone reductase (H+-translocating) / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / NADH dehydrogenase complex / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / lipid A biosynthetic process / NADH:ubiquinone reductase (H+-translocating) ...lipid-A-disaccharide synthase / lipid-A-disaccharide synthase activity / NADH:ubiquinone reductase (H+-translocating) / medium-chain fatty acid-CoA ligase activity / P450-containing electron transport chain / NADH dehydrogenase complex / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / lipid A biosynthetic process / NADH:ubiquinone reductase (H+-translocating) / NADH dehydrogenase activity / : / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport coupled proton transport / acyl binding / acyl carrier activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / : / aerobic respiration / respiratory electron transport chain / fatty acid metabolic process / mitochondrial membrane / electron transport chain / phospholipid binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / oxidoreductase activity / ribosome / protein-containing complex binding / mitochondrion / membrane / metal ion binding
Similarity search - Function
Glycosyl transferase, family 19 / Lipid-A-disaccharide synthetase / : / Dynactin subunit 5 / : / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin ...Glycosyl transferase, family 19 / Lipid-A-disaccharide synthetase / : / Dynactin subunit 5 / : / : / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Hexapeptide repeat / 2Fe-2S iron-sulfur cluster binding domain / Bacterial transferase hexapeptide (six repeats) / : / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / Thioredoxin / 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 / Trimeric LpxA-like superfamily / 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 / NADH-quinone oxidoreductase, chain G, C-terminal / : / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / SLBB domain / : / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / AMP-dependent synthetase/ligase / AMP-binding enzyme / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / 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 / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / 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 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NuoE domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Thioredoxin-like [2Fe-2S] ferredoxin / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-8Q1 / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-LPP / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER ...1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-8Q1 / ADENOSINE-5'-DIPHOSPHATE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-LPP / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / URIDINE-5'-DIPHOSPHATE / Transmembrane protein, putative / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Transmembrane protein, putative / Uncharacterized protein / Uncharacterized protein / Transmembrane protein / NADH dehydrogenase, putative / Gamma-carbonic anhydrase / Transmembrane protein / Transcription factor apfi protein, putative / Transmembrane protein, putative / Ribosomal protein L51/S25/CI-B8 domain protein / Transmembrane protein / Acyl carrier protein / NADH-ubiquinone oxidoreductase 1, chain, putative / NADH-ubiquinone oxidoreductase 24 kDa subunit / Transmembrane protein / Transmembrane protein, putative / Transmembrane protein / Uncharacterized protein / Transmembrane protein, putative / Uncharacterized protein / Zinc-finger protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NAD-dependent epimerase/dehydratase family protein / Transmembrane protein / Thioredoxin / Transmembrane protein, putative / DnaJ domain protein / lipid-A-disaccharide synthase / Transmembrane protein / Transmembrane protein, putative / Transmembrane protein / Transmembrane protein, putative / 2 iron, 2 sulfur cluster-binding protein / Transmembrane protein / Acyl carrier protein / Gamma-carbonic anhydrase / Transmembrane protein, putative / Transmembrane protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase 75 kDa subunit / Uncharacterized protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Uncharacterized protein / ETC complex I subunit motif protein / Transmembrane protein, putative / Transmembrane protein, putative / Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II / NADH-ubiquinone oxidoreductase chain 4 / Ymf62 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 5 / NADH dehydrogenase subunit 9 / Ymf58 / NADH-ubiquinone oxidoreductase chain 3 / Ymf65 / NADH dehydrogenase subunit 7 / NADH dehydrogenase subunit 2 / NADH dehydrogenase subunit 10 / Ymf57 / GRAM domain protein
Similarity search - Component
Biological speciesTetrahymena thermophila SB210 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMuhleip, A. / Kock Flygaard, R. / Amunts, A.
Funding support Sweden, European Union, 4items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchFFL15:0325 Sweden
Cancerfonden2017/1041 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
Knut and Alice Wallenberg Foundation2018.0080 Sweden
Citation
Journal: Nature / Year: 2023
Title: Structural basis of mitochondrial membrane bending by the I-II-III-IV supercomplex.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Rozbeh Baradaran / Outi Haapanen / Thomas Gruhl / Victor Tobiasson / Amandine Maréchal / Vivek Sharma / Alexey Amunts /
Abstract: Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes ...Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III-IV supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
#1: Journal: Biorxiv / Year: 2022
Title: Structural basis of mitochondrial membrane bending by I-II-III2-IV2 supercomplex
Authors: Muhleip, A. / Flygaard, R.K. / Haapanen, O. / Baradaran, R. / Gruhl, T. / Tobiasson, V. / Marechal, A. / Sharma, V. / Amunts, A.
History
DepositionSep 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 12, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A0: Lipid-A-disaccharide synthase
A1: NAD-dependent epimerase/dehydratase family protein
A2: DnaJ domain protein
A3: Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II
A4: RNase III domain-containing protein
A5: 37S ribosomal protein S25, mitochondrial
A6: Transmembrane protein, putative
A7: CX9C domain-containing protein
A8: NDUTT15
A9: Transmembrane protein, putative
AA: NADH dehydrogenase subunit 5
AB: NADH-ubiquinone oxidoreductase 75 kDa subunit
AC: NADH-ubiquinone oxidoreductase chain 4
AD: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
AE: NADH dehydrogenase subunit 7
AF: Ymf65
AG: Transcription factor apfi protein, putative
AH: NADH-ubiquinone oxidoreductase chain 1
AI: NADH-ubiquinone oxidoreductase 24 kDa subunit
AJ: Ymf62
AK: Gamma-carbonic anhydrase
AL: NADH-ubiquinone oxidoreductase 1, chain, putative
AM: Gamma-carbonic anhydrase
AN: ETC complex I subunit motif protein
AO: NADH dehydrogenase subunit 9
AP: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
AQ: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
AR: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
AS: NADH dehydrogenase, putative
AT: NADH dehydrogenase subunit 10
AU: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
AV: Acyl carrier protein
AW: Acyl carrier protein
AX: NADH-ubiquinone oxidoreductase chain 3
AY: Ymf58
AZ: Ribosomal protein L51/S25/CI-B8 domain protein
B0: Transmembrane protein, putative
B1: ATP synthase subunit e, mitochondrial
B2: GRAM domain protein
B3: Transmembrane protein, putative
B4: Transmembrane protein, putative
B5: Transmembrane protein, putative
B6: ND1b
BA: Transmembrane protein
BB: Transmembrane protein, putative
BC: NDUB8
BD: Transmembrane protein, putative
BE: NDUPH2
BF: NDUB10
BG: NDUA13
BH: NADH dehydrogenase subunit 2
BI: 2 iron, 2 sulfur cluster-binding protein
BJ: Thioredoxin
BK: COX assembly mitochondrial protein
BL: Transmembrane protein, putative
BM: Transmembrane protein, putative
BN: PH domain-containing protein
BO: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
BP: NDUB6
BQ: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
BR: Zinc-finger protein
BS: NDUB4
BT: NDUB15
BU: NDUTT16
BV: NDUTT17
BW: CHCH domain-containing protein
BX: Transmembrane protein, putative
BY: Ymf57
BZ: Complex I-MNLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,780,504146
Polymers1,714,12569
Non-polymers66,37977
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 36 types, 36 molecules A0A1A2A3A4A5A7A8AFAGAJANASAYAZB1B2B6BABCBEBFBGBIBJBKBNBPBRBS...

#1: Protein Lipid-A-disaccharide synthase


Mass: 59307.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22E24, lipid-A-disaccharide synthase
#2: Protein NAD-dependent epimerase/dehydratase family protein


Mass: 41375.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MLH2
#3: Protein DnaJ domain protein


Mass: 36878.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22DR7
#4: Protein Acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II


Mass: 36709.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24HK5
#5: Protein RNase III domain-containing protein


Mass: 35409.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7LUQ4
#6: Protein 37S ribosomal protein S25, mitochondrial


Mass: 33201.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MIJ7
#8: Protein CX9C domain-containing protein


Mass: 28412.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MMF4
#9: Protein NDUTT15


Mass: 25493.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#16: Protein Ymf65


Mass: 43146.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q951A3
#17: Protein Transcription factor apfi protein, putative


Mass: 39793.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M8Q7
#20: Protein Ymf62


Mass: 30448.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Y2
#24: Protein ETC complex I subunit motif protein


Mass: 24277.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23ND5
#29: Protein NADH dehydrogenase, putative


Mass: 20167.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M2Y3
#35: Protein Ymf58


Mass: 13509.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q950Z5
#36: Protein Ribosomal protein L51/S25/CI-B8 domain protein


Mass: 12157.782 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MA77
#38: Protein ATP synthase subunit e, mitochondrial


Mass: 11283.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22E95
#39: Protein GRAM domain protein


Mass: 10920.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: W7X4R4
#43: Protein ND1b


Mass: 7238.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#44: Protein Transmembrane protein


Mass: 24823.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MIE0
#46: Protein NDUB8


Mass: 24150.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M855
#48: Protein NDUPH2


Mass: 22446.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23KE0
#49: Protein NDUB10


Mass: 22167.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23KG0
#50: Protein NDUA13


Mass: 21045.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M2U4
#52: Protein 2 iron, 2 sulfur cluster-binding protein


Mass: 19564.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22W11
#53: Protein Thioredoxin


Mass: 19540.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22AI5
#54: Protein COX assembly mitochondrial protein


Mass: 17078.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M1N8
#57: Protein PH domain-containing protein


Mass: 15785.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22SC4
#59: Protein NDUB6


Mass: 15444.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q231G0
#61: Protein Zinc-finger protein


Mass: 15141.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MK02
#62: Protein NDUB4


Mass: 14410.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MG29
#63: Protein NDUB15


Mass: 14963.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#64: Protein NDUTT16


Mass: 15334.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#65: Protein NDUTT17


Mass: 13983.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
#66: Protein CHCH domain-containing protein


Mass: 13747.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MIM0
#68: Protein Ymf57


Mass: 12473.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / References: UniProt: Q951C2
#69: Protein Complex I-MNLL


Mass: 12103.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22W63

-
Transmembrane protein, ... , 11 types, 11 molecules A6A9B0B3B4B5BBBDBLBMBX

#7: Protein Transmembrane protein, putative


Mass: 29389.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24C39
#10: Protein Transmembrane protein, putative


Mass: 26545.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q24F24
#37: Protein Transmembrane protein, putative


Mass: 11451.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MI60
#40: Protein Transmembrane protein, putative


Mass: 9942.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: A4VD20
#41: Protein Transmembrane protein, putative


Mass: 8787.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22DC2
#42: Protein Transmembrane protein, putative


Mass: 8445.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MIK1
#45: Protein Transmembrane protein, putative


Mass: 24419.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22Z32
#47: Protein Transmembrane protein, putative


Mass: 23971.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7LT77
#55: Protein Transmembrane protein, putative


Mass: 16909.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22HE4
#56: Protein Transmembrane protein, putative


Mass: 15831.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M9B3
#67: Protein Transmembrane protein, putative


Mass: 13340.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22T55

-
NADH dehydrogenase subunit ... , 5 types, 5 molecules AAAEAOATBH

#11: Protein NADH dehydrogenase subunit 5


Mass: 88179.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q950Z0, NADH:ubiquinone reductase (H+-translocating)
#15: Protein NADH dehydrogenase subunit 7


Mass: 51227.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q951B1, NADH:ubiquinone reductase (H+-translocating)
#25: Protein NADH dehydrogenase subunit 9


Mass: 23830.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q950Z3, NADH:ubiquinone reductase (H+-translocating)
#30: Protein NADH dehydrogenase subunit 10


Mass: 18324.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q951B4, NADH:ubiquinone reductase (H+-translocating)
#51: Protein NADH dehydrogenase subunit 2


Mass: 20899.889 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q951B2, NADH:ubiquinone reductase (H+-translocating)

-
NADH-ubiquinone oxidoreductase ... , 7 types, 7 molecules ABACAHAIALAUAX

#12: Protein NADH-ubiquinone oxidoreductase 75 kDa subunit


Mass: 80580.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23KA9
#13: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 58690.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q950X9, NADH:ubiquinone reductase (H+-translocating)
#18: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 32636.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q950Y3, NADH:ubiquinone reductase (H+-translocating)
#19: Protein NADH-ubiquinone oxidoreductase 24 kDa subunit


Mass: 31216.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MEP0
#22: Protein NADH-ubiquinone oxidoreductase 1, chain, putative


Mass: 28053.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MDW5
#31: Protein NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit


Mass: 17381.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7LT42
#34: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 14416.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote)
References: UniProt: Q950Z7, NADH:ubiquinone reductase (H+-translocating)

-
NADH dehydrogenase [ubiquinone] ... , 6 types, 6 molecules ADAPAQARBOBQ

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


Mass: 52313.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210
References: UniProt: Q23KE4, NADH:ubiquinone reductase (H+-translocating)
#26: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 22890.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: A4VDQ6
#27: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial


Mass: 22698.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q233X7
#28: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 21642.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MK61
#58: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8


Mass: 15689.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q23B10
#60: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4


Mass: 15193.583 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MAF0

-
Gamma-carbonic ... , 2 types, 2 molecules AKAM

#21: Protein Gamma-carbonic anhydrase


Mass: 28216.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22XU5
#23: Protein Gamma-carbonic anhydrase


Mass: 25395.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7M6S0

-
Acyl carrier ... , 2 types, 2 molecules AVAW

#32: Protein Acyl carrier protein


Mass: 16249.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: Q22XT6
#33: Protein Acyl carrier protein


Mass: 15428.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila SB210 (eukaryote) / Strain: SB210 / References: UniProt: I7MD12

-
Non-polymers , 13 types, 77 molecules

#70: 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.: 22 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#71: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#72: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#73: Chemical...
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#74: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#75: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#76: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#77: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#78: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#79: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#81: 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.: 1 / Source method: obtained synthetically / Formula: C23H45N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#82: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: NADH:ubiquinone oxidoreductase complex (complex-I) from respiratory supercomplex of Tetrahymena thermophila
Type: COMPLEX / Entity ID: #1-#69 / Source: NATURAL
Molecular weightValue: 1.52 MDa / Experimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 25.66 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 138746 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003119625
ELECTRON MICROSCOPYf_angle_d0.66161117
ELECTRON MICROSCOPYf_dihedral_angle_d13.05446200
ELECTRON MICROSCOPYf_chiral_restr0.03916910
ELECTRON MICROSCOPYf_plane_restr0.00320116

+
About Yorodumi

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

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

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

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

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

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

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

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

+
Jul 12, 2017. Major update of PDB

Major update of PDB

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

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

-
Yorodumi

Thousand views of thousand structures

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

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

Read more