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- EMDB-4041: Structure of mammalian respiratory Complex I, class3. -

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Basic information

Entry
Database: EMDB / ID: 4041
TitleStructure of mammalian respiratory Complex I, class3.
Map dataA map of third class of bovine Complex 1.
SampleBovine Complex I
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH dehydrogenase [ubiquinone] iron-sulfur protein ...) x 7
  • (NADH dehydrogenase [ubiquinone] flavoprotein ...) x 3
  • NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 12
  • Acyl carrier protein, mitochondrial
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 11
  • (ligand) x 5
Function / homologyNADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-quinone oxidoreductase, chain I / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH-quinone oxidoreductase, chain G, C-terminal / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, MNLL subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain ...NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / NADH-quinone oxidoreductase, chain I / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH-quinone oxidoreductase, chain G, C-terminal / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, MNLL subunit / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 2, C-terminal / CHCH / NADH:ubiquinone oxidoreductase, subunit G / NADH-quinone oxidoreductase, chain M/4 / NADH dehydrogenase, subunit C / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Molybdopterin oxidoreductase, 4Fe-4S domain / NADH-plastoquinone oxidoreductase, chain 5 / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Phosphopantetheine attachment site / Molybdopterin oxidoreductase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / Ribosomal protein/NADH dehydrogenase domain / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Complex 1 LYR protein / NADH:ubiquinone oxidoreductase, B18 subunit / Phosphopantetheine binding ACP domain / GRIM-19 / NADH:ubiquinone oxidoreductase, subunit b14.5b / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, chain 2 / Deoxynucleoside kinase domain / Proton-conducting membrane transporter / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH dehydrogenase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / ACP-like superfamily / Thioredoxin-like superfamily / 2Fe-2S ferredoxin-like superfamily / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / [NiFe]-hydrogenase, large subunit / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Zinc finger, CHCC-type / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, ESSS subunit / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH-ubiquinone oxidoreductase, subunit 10 / Soluble ligand binding domain / P-loop containing nucleoside triphosphate hydrolase / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase / Acyl carrier protein (ACP) / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase subunit 10 / Zinc-finger domain / SLBB domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / 4Fe-4S dicluster domain / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH-ubiquinone oxidoreductase MWFE subunit / Phosphopantetheine attachment site. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Complex I biogenesis / Neutrophil degranulation / Respiratory electron transport / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Carrier protein (CP) domain profile. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature.
Function and homology information
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 5.6 Å resolution
AuthorsVinothkumar KR / Zhu J
CitationJournal: Nature / Year: 2016
Title: Structure of mammalian respiratory complex I.
Authors: Jiapeng Zhu / Kutti R Vinothkumar / Judy Hirst
Validation ReportPDB-ID: 5ldx

SummaryFull reportAbout validation report
DateDeposition: Jun 28, 2016 / Header (metadata) release: Aug 10, 2016 / Map release: Sep 14, 2016 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.125
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.125
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5ldx
  • Surface level: 0.125
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4041.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.33 Å/pix.
= 478.8 Å
360 pix
1.33 Å/pix.
= 478.8 Å
360 pix
1.33 Å/pix.
= 478.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density
Contour Level:0.125 (by author), 0.125 (movie #1):
Minimum - Maximum-0.09520442 - 0.67937535
Average (Standard dev.)7.317136E-5 (0.01833591)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin000
Limit359359359
Spacing360360360
CellA=B=C: 478.80002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z478.800478.800478.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0950.6790.000

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Supplemental data

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Sample components

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Entire Bovine Complex I

EntireName: Bovine Complex I
Details: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits.
Number of components: 50
MassTheoretical: 1000 kDa

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Component #1: protein, Bovine Complex I

ProteinName: Bovine Complex I
Details: Complex I is the first enzyme in the electron transport chain located in the inner membrane of mitochondria and in higher eukaryotes, it is a multi-subunit membrane protein complex, consisting of >40 subunits.
Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondria

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Component #2: protein, NADH-ubiquinone oxidoreductase chain 3

ProteinName: NADH-ubiquinone oxidoreductase chain 3 / Recombinant expression: No
MassTheoretical: 13.058521 kDa
SourceSpecies: Bos taurus (cattle)

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Component #3: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
Details: This chain coordinates a Iron-sulphur cluster. / Recombinant expression: No
MassTheoretical: 20.104531 kDa
SourceSpecies: Bos taurus (cattle)

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Component #4: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
Recombinant expression: No
MassTheoretical: 26.464807 kDa
SourceSpecies: Bos taurus (cattle)

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Component #5: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial
Details: 128 should be an R instead of Q for Cambridge cows.
Recombinant expression: No
MassTheoretical: 49.165289 kDa
SourceSpecies: Bos taurus (cattle)

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Component #6: protein, NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
Details: This chain coordinates FES / Recombinant expression: No
MassTheoretical: 23.840361 kDa
SourceSpecies: Bos taurus (cattle)

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Component #7: protein, NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
Details: This chain coordinates 1SF4 and binds FMN / Recombinant expression: No
MassTheoretical: 48.562137 kDa
SourceSpecies: Bos taurus (cattle)

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Component #8: protein, NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochond...

ProteinName: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial,NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
Details: This chain coordinates 2 SF4 and 1FES / Recombinant expression: No
MassTheoretical: 64.614125 kDa
SourceSpecies: Bos taurus (cattle)

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Component #9: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1 / Recombinant expression: No
MassTheoretical: 35.688773 kDa
SourceSpecies: Bos taurus (cattle)

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Component #10: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial
Details: This chain coordinates 2x SF4 / Recombinant expression: No
MassTheoretical: 20.219947 kDa
SourceSpecies: Bos taurus (cattle)

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Component #11: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6 / Recombinant expression: No
MassTheoretical: 19.082479 kDa
SourceSpecies: Bos taurus (cattle)

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Component #12: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Recombinant expression: No
MassTheoretical: 10.800186 kDa
SourceSpecies: Bos taurus (cattle)

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Component #13: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5
Details: Note: The density for transverse helix and the last TM helix around 548-605 is poor but has been left as observed for class 1 for comparison.
Recombinant expression: No
MassTheoretical: 68.327922 kDa
SourceSpecies: Bos taurus (cattle)

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Component #14: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Recombinant expression: No
MassTheoretical: 52.13075 kDa
SourceSpecies: Bos taurus (cattle)

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Component #15: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Recombinant expression: No
MassTheoretical: 39.27493 kDa
SourceSpecies: Bos taurus (cattle)

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Component #16: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Recombinant expression: No
MassTheoretical: 34.014227 kDa
SourceSpecies: Bos taurus (cattle)

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Component #17: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, NDUFA9
Details: binds NAP / Recombinant expression: No
MassTheoretical: 24.102582 kDa
SourceSpecies: Bos taurus (cattle)

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Component #18: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, NDUFS4
Recombinant expression: No
MassTheoretical: 9.634868 kDa
SourceSpecies: Bos taurus (cattle)

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Component #19: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, m...

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
Recombinant expression: No
MassTheoretical: 8.316853 kDa
SourceSpecies: Bos taurus (cattle)

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Component #20: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
Recombinant expression: No
MassTheoretical: 11.097824 kDa
SourceSpecies: Bos taurus (cattle)

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Component #21: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Recombinant expression: No
MassTheoretical: 10.119541 kDa
SourceSpecies: Bos taurus (cattle)

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Component #22: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
Recombinant expression: No
MassTheoretical: 13.203414 kDa
SourceSpecies: Bos taurus (cattle)

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Component #23: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 14.952349 kDa
SourceSpecies: Bos taurus (cattle)

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Component #24: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Recombinant expression: No
MassTheoretical: 17.617576 kDa
SourceSpecies: Bos taurus (cattle)

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Component #25: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Details: The density for this subunit is poor and the model has been taken from class1 for comparison.
Recombinant expression: No
MassTheoretical: 14.640825 kDa
SourceSpecies: Bos taurus (cattle)

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Component #26: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Recombinant expression: No
MassTheoretical: 14.1359 kDa
SourceSpecies: Bos taurus (cattle)

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Component #27: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 8.117445 kDa
SourceSpecies: Bos taurus (cattle)

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Component #28: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3,NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3
Recombinant expression: No
MassTheoretical: 7.860488 kDa
SourceSpecies: Bos taurus (cattle)

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Component #29: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Recombinant expression: No
MassTheoretical: 5.836698 kDa
SourceSpecies: Bos taurus (cattle)

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Component #30: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydr...

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2,NADH dehydrogenase [ubiquinone] 1 subunit C2
Recombinant expression: No
MassTheoretical: 11.9883 kDa
SourceSpecies: Bos taurus (cattle)

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Component #31: protein, NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

ProteinName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Recombinant expression: No
MassTheoretical: 12.694671 kDa
SourceSpecies: Bos taurus (cattle)

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Component #32: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Recombinant expression: No
MassTheoretical: 6.978148 kDa
SourceSpecies: Bos taurus (cattle)

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Component #33: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Recombinant expression: No
MassTheoretical: 14.469059 kDa
SourceSpecies: Bos taurus (cattle)

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Component #34: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Recombinant expression: No
MassTheoretical: 12.614555 kDa
SourceSpecies: Bos taurus (cattle)

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Component #35: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Recombinant expression: No
MassTheoretical: 10.234333 kDa
SourceSpecies: Bos taurus (cattle)

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Component #36: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, NDUFB2
Recombinant expression: No
MassTheoretical: 4.443468 kDa
SourceSpecies: Bos taurus (cattle)

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Component #37: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3, NDUFB3
Recombinant expression: No
MassTheoretical: 6.315777 kDa
SourceSpecies: Bos taurus (cattle)

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Component #38: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, NDUFB8
Recombinant expression: No
MassTheoretical: 10.060393 kDa
SourceSpecies: Bos taurus (cattle)

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Component #39: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
Recombinant expression: No
MassTheoretical: 13.415493 kDa
SourceSpecies: Bos taurus (cattle)

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Component #40: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
Recombinant expression: No
MassTheoretical: 19.246094 kDa
SourceSpecies: Bos taurus (cattle)

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Component #41: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
Recombinant expression: No
MassTheoretical: 7.5839 kDa
SourceSpecies: Bos taurus (cattle)

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Component #42: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10,NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
Recombinant expression: No
MassTheoretical: 16.906949 kDa
SourceSpecies: Bos taurus (cattle)

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Component #43: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
Recombinant expression: No
MassTheoretical: 16.309545 kDa
SourceSpecies: Bos taurus (cattle)

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Component #44: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7, NDUFA7
Recombinant expression: No
MassTheoretical: 7.42214 kDa
SourceSpecies: Bos taurus (cattle)

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Component #45: protein, NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3

ProteinName: NADH dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3
Recombinant expression: No
MassTheoretical: 2.996685 kDa
SourceSpecies: Bos taurus (cattle)

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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, 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 #48: ligand, FLAVIN MONONUCLEOTIDE

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

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Component #49: ligand, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.743405 kDa

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Component #50: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3.5 mg/ml / pH: 8
Support filmholey carbon grids were placed on a filter paper in a glass petridish and pumped for around 5 minutes to remove any residual moisture. the glow of the plasma was observed and glow discharged when it was purple
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %
Details: The specimen was vitrified in an environmental plunge-freeze apparatus, blot for 12-15 seconds after the diameter of the blotted meniscus ceases to spread and plunged.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal), 105263 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800 - 5500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 85 - 85 K)
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 14 microns
Details: Images were collected in movie mode at 17 frames per second. Thus each frame has ~1.0 e/A2s

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 19306
Details: Each image was exposed for 2 seconds resulting in a total dose of ~35 e/A2s. The frames were captures with a in-house protocol at 17 frames/second.
3D reconstructionSoftware: RELION
CTF correction: Ctf was corrected per particle. Ctf was estimated on the whole micrograph
Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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About Yorodumi

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News

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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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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

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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