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- EMDB-4479: CI Membrane Arm focused refinement from Ovine respiratory SC I+III2 -

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Basic information

Entry
Database: EMDB / ID: EMD-4479
TitleCI Membrane Arm focused refinement from Ovine respiratory SC I+III2
Map data
SampleOvine mitochondrial SC I+III2
  • NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
  • (NADH-ubiquinone oxidoreductase chain ...) x 7
  • (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit ...) x 5
  • (NADH:ubiquinone oxidoreductase subunit ...) x 9
  • Acyl carrier protein
  • (NADH dehydrogenase [ubiquinone] 1 subunit ...) x 2
  • (NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit ...) x 4
  • (ligand) x 4
Function / homology
Function and homology information


cellular response to oxygen levels / gliogenesis / neural precursor cell proliferation / NADH:ubiquinone reductase (H+-translocating) / oxygen sensor activity / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport ...cellular response to oxygen levels / gliogenesis / neural precursor cell proliferation / NADH:ubiquinone reductase (H+-translocating) / oxygen sensor activity / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial large ribosomal subunit / electron transport chain / quinone binding / reactive oxygen species metabolic process / respirasome / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / mitochondrial matrix / protein-containing complex binding / integral component of membrane / nucleoplasm
Similarity search - Function
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) ...NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase 1 alpha subcomplex subunit 3 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase subunit 5, C-terminal / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / Deoxynucleoside kinase / Deoxynucleoside kinase domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain 5-like / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / Proton-conducting membrane transporter / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / CHCH / CHCH domain / [NiFe]-hydrogenase, large subunit / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Complex I-49kD / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ESSS / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-B17 / Complex I-15 kDa / Complex I-B12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-B15 / Complex I-MNLL ...Complex I-49kD / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ESSS / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / Complex I-B17 / Complex I-15 kDa / Complex I-B12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / Complex I-B15 / Complex I-MNLL / Complex I-AGGG / NADH-ubiquinone oxidoreductase chain 2 / Complex I-B22 / Complex I-B14.7 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / Complex I-B18 / Complex I-B9 / Acyl carrier protein / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / Complex I-SGDH
Similarity search - Component
Biological speciesOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLetts JA / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 17, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q9b
  • Surface level: 0.14
  • 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_4479.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 512 pix.
= 716.8 Å
1.4 Å/pix.
x 512 pix.
= 716.8 Å
1.4 Å/pix.
x 512 pix.
= 716.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.31848875 - 0.5837337
Average (Standard dev.)0.00000054276 (±0.013065267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 716.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z716.800716.800716.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.3180.5840.000

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Supplemental data

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Segmentation: #1

Fileemd_4479_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Focused refinement around CI membrane arm of ovine...

Fileemd_4479_half_map_1.map
AnnotationFocused refinement around CI membrane arm of ovine SC I III2. Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Focused refinement around CI membrane arm of ovine...

Fileemd_4479_half_map_2.map
AnnotationFocused refinement around CI membrane arm of ovine SC I III2. Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Ovine mitochondrial SC I+III2

EntireName: Ovine mitochondrial SC I+III2
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Number of Components: 34

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Component #1: protein, Ovine mitochondrial SC I+III2

ProteinName: Ovine mitochondrial SC I+III2
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Recombinant expression: No
MassTheoretical: 1.4 MDa
SourceSpecies: Ovis aries (sheep)
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane / Organ Or Tissue: Heart

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Component #2: protein, NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiq...

ProteinName: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
Details: Since this is a focused refinement only the N-terminal part of this subunit is present in the density.,Since this is a focused refinement only the N-terminal part of this subunit is present in the density.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.193273 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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

ProteinName: NADH-ubiquinone oxidoreductase chain 3
Details: There is a disordered region in the protein that is not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.10652 kDa
SourceSpecies: Sheep (sheep)

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Component #4: protein, NADH-ubiquinone oxidoreductase chain 1

ProteinName: NADH-ubiquinone oxidoreductase chain 1
Details: There is a disordered region in the protein that is not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.884902 kDa
SourceSpecies: Sheep (sheep)

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Component #5: protein, NADH-ubiquinone oxidoreductase chain 6

ProteinName: NADH-ubiquinone oxidoreductase chain 6
Details: There is a disordered region in the protein that was not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.126619 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #6: protein, NADH-ubiquinone oxidoreductase chain 4L

ProteinName: NADH-ubiquinone oxidoreductase chain 4L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.840228 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #7: protein, NADH-ubiquinone oxidoreductase chain 5

ProteinName: NADH-ubiquinone oxidoreductase chain 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.410898 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #8: protein, NADH-ubiquinone oxidoreductase chain 4

ProteinName: NADH-ubiquinone oxidoreductase chain 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.058734 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #9: protein, NADH-ubiquinone oxidoreductase chain 2

ProteinName: NADH-ubiquinone oxidoreductase chain 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.149805 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #10: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.610776 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #11: protein, NADH:ubiquinone oxidoreductase subunit B5

ProteinName: NADH:ubiquinone oxidoreductase subunit B5
Details: First few residues are disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.714369 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #12: protein, Acyl carrier protein

ProteinName: Acyl carrier protein
Details: The first residue is disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.119541 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #13: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.008014 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #14: protein, NADH:ubiquinone oxidoreductase subunit B10

ProteinName: NADH:ubiquinone oxidoreductase subunit B10
Details: Some residues are disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.880752 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #15: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.803762 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #16: protein, NADH:ubiquinone oxidoreductase subunit S5

ProteinName: NADH:ubiquinone oxidoreductase subunit S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.474397 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #17: protein, NADH:ubiquinone oxidoreductase subunit A3

ProteinName: NADH:ubiquinone oxidoreductase subunit A3
Details: The N-terminus is disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.194655 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #18: protein, NADH:ubiquinone oxidoreductase subunit B3

ProteinName: NADH:ubiquinone oxidoreductase subunit B3
Details: The termini are disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.015482 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #19: protein, NADH dehydrogenase [ubiquinone] 1 subunit C2

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C2
Details: The N-terminal residue is disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.23142 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #20: protein, NADH:ubiquinone oxidoreductase subunit B4

ProteinName: NADH:ubiquinone oxidoreductase subunit B4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.975999 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #21: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Details: Because this is a focused refinement only the C-terminal part of this subunit is present in the density.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.635264 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #22: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
Details: Disordered regions of this subunit were not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.433929 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #23: protein, NADH:ubiquinone oxidoreductase subunit B7

ProteinName: NADH:ubiquinone oxidoreductase subunit B7
Details: The C-terminus of this subunit was disordered and therefore not modeled
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.28261 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #24: protein, NADH:ubiquinone oxidoreductase subunit B9

ProteinName: NADH:ubiquinone oxidoreductase subunit B9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.648715 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #25: protein, NADH:ubiquinone oxidoreductase subunit B2

ProteinName: NADH:ubiquinone oxidoreductase subunit B2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.500289 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #26: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.81807 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #27: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subuni...

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
Details: The N-terminus was disordered and therefore not modeled.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.455033 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #28: protein, NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial

ProteinName: NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.808645 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #29: protein, NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.930083 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #30: protein, NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

ProteinName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.211519 kDa
SourceSpecies: Sheep (sheep)
Source (natural)Organ Or Tissue: Heart

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Component #31: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Component #32: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

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Component #33: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.790145 kDa

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Component #34: ligand, S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)but...

LigandName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.568704 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL
Buffer solution: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: PROPANE / Temperature: 277 K / Humidity: 95 %
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing.

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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: 51 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 1854

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 174334
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.9 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1LNK
Overall BValue: 90
Output model

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  • 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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