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- PDB-6x89: Vigna radiata mitochondrial complex I* -

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Basic information

Entry
Database: PDB / ID: 6x89
TitleVigna radiata mitochondrial complex I*
Components
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 8
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 2
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 5
  • (Unknown Peptide) x 3
  • (gamma carbonic anhydrase 1, ...) x 2
  • NDUA7
  • NDUC2
  • NDUS2
  • NDUS3
  • NDUX1
  • NU1M
  • NU2M
  • NU3M
  • NU4L
  • NU6M
  • Protein At2g27730, mitochondrial
  • gamma carbonic anhydrase-like 2, mitochondrial
  • serine/arginine-rich-splicing factor SR34 isoform X2
  • uncharacterized protein LOC106754061
KeywordsMEMBRANE PROTEIN / respiration / mitochondria / electron transport chain / complex I
Function / homology
Function and homology information


NADH dehydrogenase activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration ...NADH dehydrogenase activity / electron transport coupled proton transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / mRNA processing / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / mRNA binding / protein-containing complex binding / mitochondrion / metal ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
At2g27730-like / : / : / : / Hexapeptide repeat of succinyl-transferase / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / : / SLBB domain / Hexapeptide repeat ...At2g27730-like / : / : / : / Hexapeptide repeat of succinyl-transferase / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / : / SLBB domain / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / NADH-ubiquinone oxidoreductase MWFE subunit / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / GRIM-19 / GRIM-19 protein / 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 / Trimeric LpxA-like superfamily / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / : / SLBB domain / : / 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 / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / 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 / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / 2Fe-2S iron-sulfur cluster binding domain / NAD-dependent epimerase/dehydratase / NuoE domain / NAD dependent epimerase/dehydratase family / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / CHCH / CHCH domain / NADH-quinone oxidoreductase subunit E, N-terminal / 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 / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Thioredoxin-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Uncharacterized protein LOC106754061 / Uncharacterized protein At2g27730, mitochondrial / Serine/arginine-rich-splicing factor SR34 isoform X2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / IRON/SULFUR CLUSTER / Uncharacterized protein LOC106754061 / Uncharacterized protein At2g27730, mitochondrial / Serine/arginine-rich-splicing factor SR34 isoform X2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial-like / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Gamma carbonic anhydrase-like 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Uncharacterized protein LOC106767534 / Uncharacterized protein LOC106768957 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / 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 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLetts, J.A. / Maldonado, M. / Padavannil, A. / Zhou, L. / Guo, F.
CitationJournal: Elife / Year: 2020
Title: Atomic structure of a mitochondrial complex I intermediate from vascular plants.
Authors: Maria Maldonado / Abhilash Padavannil / Long Zhou / Fei Guo / James A Letts /
Abstract: Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large ...Respiration, an essential metabolic process, provides cells with chemical energy. In eukaryotes, respiration occurs via the mitochondrial electron transport chain (mETC) composed of several large membrane-protein complexes. Complex I (CI) is the main entry point for electrons into the mETC. For plants, limited availability of mitochondrial material has curbed detailed biochemical and structural studies of their mETC. Here, we present the cryoEM structure of the known CI assembly intermediate CI* from at 3.9 Å resolution. CI* contains CI's NADH-binding and CoQ-binding modules, the proximal-pumping module and the plant-specific γ-carbonic-anhydrase domain (γCA). Our structure reveals significant differences in core and accessory subunits of the plant complex compared to yeast, mammals and bacteria, as well as the details of the γCA domain subunit composition and membrane anchoring. The structure sheds light on differences in CI assembly across lineages and suggests potential physiological roles for CI* beyond assembly.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Unknown Peptide
A2: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
A5: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
A6: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
A7: NDUA7
A9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1
AL: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
S1: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
S2: NDUS2
S3: NDUS3
S4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
S6: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
S7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
S8: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
V1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
V2: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
1M: NU1M
2M: NU2M
3M: NU3M
4L: NU4L
6M: NU6M
A1: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
A3: uncharacterized protein LOC106754061
A8: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
AM: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
B: Unknown Peptide
C: Unknown Peptide
C2: NDUC2
P2: Protein At2g27730, mitochondrial
S5: serine/arginine-rich-splicing factor SR34 isoform X2
X1: NDUX1
G1: gamma carbonic anhydrase 1, mitochondrial
G2: gamma carbonic anhydrase 1, mitochondrial-like
L2: gamma carbonic anhydrase-like 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)790,32452
Polymers781,79134
Non-polymers8,53318
Water00
1


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

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Components

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Protein/peptide , 3 types, 3 molecules ABC

#1: Protein/peptide Unknown Peptide


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#26: Protein/peptide Unknown Peptide


Mass: 2145.636 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#27: Protein/peptide Unknown Peptide


Mass: 3677.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)

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NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ... , 8 types, 8 molecules A2A5A6A9ALA1A8AM

#2: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 10884.632 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TVC7
#3: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial


Mass: 18977.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3U023
#4: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6


Mass: 14920.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3W1K8
#6: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1


Mass: 43781.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3V8W7
#7: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 18192.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VNK7
#22: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1


Mass: 7357.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TU57
#24: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B


Mass: 12022.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VVN6
#25: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A


Mass: 16189.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UYW0

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Protein , 14 types, 14 molecules A7S2S31M2M3M4L6MA3C2P2S5X1L2

#5: Protein NDUA7


Mass: 14356.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UVC7
#9: Protein NDUS2


Mass: 44813.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#10: Protein NDUS3


Mass: 22806.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#17: Protein NU1M


Mass: 35651.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#18: Protein NU2M


Mass: 53900.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#19: Protein NU3M


Mass: 13507.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#20: Protein NU4L


Mass: 11082.356 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#21: Protein NU6M


Mass: 23484.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean)
#23: Protein uncharacterized protein LOC106754061


Mass: 6695.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TCK0
#28: Protein NDUC2


Mass: 9130.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UPL8
#29: Protein Protein At2g27730, mitochondrial


Mass: 12172.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3TGE7
#30: Protein serine/arginine-rich-splicing factor SR34 isoform X2


Mass: 45640.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQ33
#31: Protein NDUX1


Mass: 10949.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VI15
#34: Protein gamma carbonic anhydrase-like 2, mitochondrial


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

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NADH dehydrogenase [ubiquinone] iron-sulfur protein ... , 5 types, 5 molecules S1S4S6S7S8

#8: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial


Mass: 81434.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3TQ85
#11: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial


Mass: 16435.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3UIW7
#12: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial


Mass: 11582.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3VYF3
#13: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial


Mass: 23710.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata / References: UniProt: A0A1S3U8J5
#14: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial


Mass: 25545.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VGS8

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NADH dehydrogenase [ubiquinone] flavoprotein ... , 2 types, 2 molecules V1V2

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


Mass: 53817.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata
References: UniProt: A0A1S3V7V2, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#16: Protein NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial


Mass: 27992.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3U769

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Gamma carbonic anhydrase 1, ... , 2 types, 2 molecules G1G2

#32: Protein gamma carbonic anhydrase 1, mitochondrial


Mass: 29333.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vigna radiata (mung bean) / References: UniProt: A0A1S3VT00
#33: Protein gamma carbonic anhydrase 1, mitochondrial-like


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

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Non-polymers , 6 types, 18 molecules

#35: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#36: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#37: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#39: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#40: 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 complex I* / Type: COMPLEX
Details: Complex I 800 kDa assembly intermediate (complex I*)
Entity ID: #1-#34 / Source: NATURAL
Molecular weightValue: 0.8 MDa / Experimental value: NO
Source (natural)Organism: Vigna radiata (mung bean)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
30.1 %digitonindigitonin1
41 mMEDTAedta1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Extracted from V. radiata mitochondrial membranes with digitonin, exchanged into amphipole A8-35, purified on sucrose gradient.
Specimen supportDetails: 30 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: Blotted for 9 seconds at 100% humidity, 15 degrees C.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 3 sec. / Electron dose: 86.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9816

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 190951
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34407 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01146141
ELECTRON MICROSCOPYf_angle_d1.58762663
ELECTRON MICROSCOPYf_dihedral_angle_d16.7776531
ELECTRON MICROSCOPYf_chiral_restr0.0676934
ELECTRON MICROSCOPYf_plane_restr0.0088024

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  • 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

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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

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