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- EMDB-11614: Plant mitochondrial respiratory complex I -

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Basic information

Entry
Database: EMDB / ID: EMD-11614
TitlePlant mitochondrial respiratory complex I
Map data
SampleMitochondrial respiratory complex I:
51kDa / Nad2m / Nad3m / Nad6m / Nad1m / Nad4Lm / PGIV / B16.6 / MWFE / B9 ...51kDa / Nad2m / Nad3m / Nad6m / Nad1m / Nad4Lm / PGIV / B16.6 / MWFE / B9 / B14.5a / B14.5b / 15kDa / Nad7m / 75kDa / 39kDa / Nad9m / 24kDa / 18kDa / 13kDa / B13 / B17.2 / PSST / TYKY / B14 / 20.9kDa / B8 / ACPM1 / Unk1 / P2 / CAL1 / CA1 / Nad4m / PDSW / ESSS / B22 / Nad5m / B18 / AGGG / ACPM2 / B15 / Unk2 / P1 / B12-1 / (ligand) x 10
Function / homology
Function and homology information


respiratory chain complex I / NADH dehydrogenase complex / cold acclimation / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases / embryo development ending in seed dormancy / photorespiration / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I ...respiratory chain complex I / NADH dehydrogenase complex / cold acclimation / ubiquinone-6 biosynthetic process / Lyases; Carbon-oxygen lyases; Hydro-lyases / embryo development ending in seed dormancy / photorespiration / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / acyl binding / acyl carrier activity / electron transport coupled proton transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / ubiquinone binding / electron transport chain / plastid / NADH dehydrogenase (ubiquinone) activity / vacuolar membrane / vacuole / cobalt ion binding / quinone binding / protein homotrimerization / aerobic respiration / response to osmotic stress / respirasome / respiratory electron transport chain / mitochondrial membrane / chloroplast / 2 iron, 2 sulfur cluster binding / fatty acid biosynthetic process / mitochondrial intermembrane space / carbonate dehydratase activity / peroxisome / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / copper ion binding / oxidation-reduction process / mitochondrial matrix / electron transfer activity / carbohydrate metabolic process / nucleolus / mitochondrion / zinc ion binding / integral component of membrane / extracellular region / plasma membrane / metal ion binding / nucleus / cytosol
NADH:ubiquinone oxidoreductase, subunit G / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, subunit D / NADH-ubiquinone oxidoreductase chain 4L/K / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-quinone oxidoreductase, chain I ...NADH:ubiquinone oxidoreductase, subunit G / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-quinone oxidoreductase, subunit D / NADH-ubiquinone oxidoreductase chain 4L/K / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-quinone oxidoreductase, chain I / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-quinone oxidoreductase, chain M/4 / CHCH / NADH dehydrogenase subunit 5, C-terminal / Trimeric LpxA-like superfamily / NADH ubiquinone oxidoreductase, F subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Hexapeptide repeat / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / GRIM-19 / Molybdopterin oxidoreductase / NADH:ubiquinone oxidoreductase, B18 subunit / Complex 1 LYR protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Ribosomal protein/NADH dehydrogenase domain / Molybdopterin oxidoreductase, 4Fe-4S domain / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Phosphopantetheine attachment site / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase / Acyl carrier protein (ACP) / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, chain G, C-terminal / NAD(P)-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase 11kDa subunit / 2Fe-2S ferredoxin-like superfamily / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily / ACP-like superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NuoE domain / [NiFe]-hydrogenase, large subunit / NAD(P)H-quinone oxidoreductase subunit D/H / Phosphopantetheine binding ACP domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Zinc finger, CHCC-type / Soluble ligand binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / Gamma carbonic anhydrase-like 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial / At1g67350 / At2g46540/F11C10.23 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B ...NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / Gamma carbonic anhydrase-like 1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-B, mitochondrial / At1g67350 / At2g46540/F11C10.23 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-A / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-B / Furry / AT2G31490 protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / Acyl carrier protein 2, mitochondrial / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 3 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / NADH-ubiquinone oxidoreductase chain 4 / At4g16450 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Excitatory amino acid transporter / Uncharacterized protein At2g27730, mitochondrial
Biological speciesBrassica oleracea (wild cabbage) / Wild cabbage (wild cabbage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSoufari H / Waltz F / Hashem Y
Funding support France, 2 items
OrganizationGrant numberCountry
French National Research AgencyANR-16-CE11-0024-02 France
European Research Council (ERC)759120
CitationJournal: Nat Commun / Year: 2020
Title: Specific features and assembly of the plant mitochondrial complex I revealed by cryo-EM.
Authors: Heddy Soufari / Camila Parrot / Lauriane Kuhn / Florent Waltz / Yaser Hashem /
Abstract: Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the ...Mitochondria are the powerhouses of eukaryotic cells and the site of essential metabolic reactions. Complex I or NADH:ubiquinone oxidoreductase is the main entry site for electrons into the mitochondrial respiratory chain and constitutes the largest of the respiratory complexes. Its structure and composition vary across eukaryote species. However, high resolution structures are available only for one group of eukaryotes, opisthokonts. In plants, only biochemical studies were carried out, already hinting at the peculiar composition of complex I in the green lineage. Here, we report several cryo-electron microscopy structures of the plant mitochondrial complex I. We describe the structure and composition of the plant respiratory complex I, including the ancestral mitochondrial domain composed of the carbonic anhydrase. We show that the carbonic anhydrase is a heterotrimeric complex with only one conserved active site. This domain is crucial for the overall stability of complex I as well as a peculiar lipid complex composed of cardiolipin and phosphatidylinositols. Moreover, we also describe the structure of one of the plant-specific complex I assembly intermediates, lacking the whole P module, in presence of the maturation factor GLDH. GLDH prevents the binding of the plant specific P1 protein, responsible for the linkage of the P to the P module.
Validation ReportPDB-ID: 7a23

SummaryFull reportAbout validation report
History
DepositionAug 15, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7a23
  • Surface level: 0.0235
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11614.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 360 pix.
= 399.6 Å
1.11 Å/pix.
x 360 pix.
= 399.6 Å
1.11 Å/pix.
x 360 pix.
= 399.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.0235 / Movie #1: 0.0235
Minimum - Maximum-0.07923831 - 0.2573688
Average (Standard dev.)-0.0000399379 (±0.005220195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 399.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z399.600399.600399.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0790.257-0.000

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Supplemental data

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Sample components

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Entire Mitochondrial respiratory complex I

EntireName: Mitochondrial respiratory complex I / Number of components: 55

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Component #1: protein, Mitochondrial respiratory complex I

ProteinName: Mitochondrial respiratory complex I / Recombinant expression: No
SourceSpecies: Brassica oleracea (wild cabbage)
Source (natural)Organelle: Mitochondria / Organ or tissue: Flower

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Component #2: protein, 51kDa

ProteinName: 51kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.522418 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #3: protein, Nad2m

ProteinName: Nad2m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.486836 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #4: protein, Nad3m

ProteinName: Nad3m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.941387 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #5: protein, Nad6m

ProteinName: Nad6m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.700422 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #6: protein, Nad1m

ProteinName: Nad1m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.049086 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #7: protein, Nad4Lm

ProteinName: Nad4Lm / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.139469 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #8: protein, PGIV

ProteinName: PGIV / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.985954 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #9: protein, B16.6

ProteinName: B16.6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.145584 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #10: protein, MWFE

ProteinName: MWFE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.349628 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #11: protein, B9

ProteinName: B9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.810177 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #12: protein, B14.5a

ProteinName: B14.5a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.060062 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #13: protein, B14.5b

ProteinName: B14.5b / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.220749 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #14: protein, 15kDa

ProteinName: 15kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.914133 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #15: protein, Nad7m

ProteinName: Nad7m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.020801 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #16: protein, 75kDa

ProteinName: 75kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 81.619367 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #17: protein, 39kDa

ProteinName: 39kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.988652 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #18: protein, Nad9m

ProteinName: Nad9m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.91091 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #19: protein, 24kDa

ProteinName: 24kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.423607 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #20: protein, 18kDa

ProteinName: 18kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.160445 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #21: protein, 13kDa

ProteinName: 13kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.251122 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #22: protein, B13

ProteinName: B13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.201906 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #23: protein, B17.2

ProteinName: B17.2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.346736 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #24: protein, PSST

ProteinName: PSST / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.071949 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #25: protein, TYKY

ProteinName: TYKY / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.410662 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #26: protein, B14

ProteinName: B14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.102261 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #27: protein, 20.9kDa

ProteinName: 20.9kDa / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.355008 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #28: protein, B8

ProteinName: B8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.865765 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #29: protein, ACPM1

ProteinName: ACPM1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.735628 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #30: protein, Unk1

ProteinName: Unk1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.723883 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #31: protein, P2

ProteinName: P2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.96552 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #32: protein, CAL1

ProteinName: CAL1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.599748 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #33: protein, CA1

ProteinName: CA1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 30.010039 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #34: protein, Nad4m

ProteinName: Nad4m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.869473 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #35: protein, PDSW

ProteinName: PDSW / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.555425 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #36: protein, ESSS

ProteinName: ESSS / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.680462 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #37: protein, B22

ProteinName: B22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.638335 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #38: protein, Nad5m

ProteinName: Nad5m / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.36175 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #39: protein, B18

ProteinName: B18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.757832 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #40: protein, AGGG

ProteinName: AGGG / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.58259 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #41: protein, ACPM2

ProteinName: ACPM2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.183111 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #42: protein, B15

ProteinName: B15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.305539 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #43: protein, Unk2

ProteinName: Unk2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.439571 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #44: protein, P1

ProteinName: P1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.808244 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #45: protein, B12-1

ProteinName: B12-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.239437 kDa
SourceSpecies: Wild cabbage (wild cabbage)

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Component #46: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #47: ligand, FLAVIN MONONUCLEOTIDE

LigandName: FLAVIN MONONUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.456344 kDa

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Component #48: ligand, Phosphatidylinositol

LigandName: Phosphatidylinositol / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.887128 kDa

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Component #49: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

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Component #50: ligand, UBIQUINONE-10

LigandName: UBIQUINONE-10Coenzyme Q10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.863343 kDa

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Component #51: ligand, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALM...

LigandName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.720012 kDa

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Component #52: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #53: ligand, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.745421 kDa

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Component #54: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #55: ligand, BICARBONATE ION

LigandName: BICARBONATE IONBicarbonate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.101705 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 65018
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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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. See below links for details.
  • 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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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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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.

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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