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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.
SampleBovine Complex I
SourceBos taurus / mammal / ウシ /
Map dataA map of third class of bovine Complex 1.
Methodsingle particle reconstruction, at 5.6 Å resolution
AuthorsVinothkumar KR / Zhu J
CitationNature, 2016, 536, 354-358

Nature, 2016, 536, 354-358 Yorodumi Papers
Structure of mammalian respiratory complex I.
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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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 package.

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 / mammal / ウシ /
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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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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 / mammal / ウシ /

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Component #46: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/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

Specimen stateparticle
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 assessment)

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Atomic model buiding

Output model

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