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- EMDB-22449: Plant mitochondrial supercomplex III2+IV from Vigna radiata -

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Basic information

Entry
Database: EMDB / ID: EMD-22449
TitlePlant mitochondrial supercomplex III2+IV from Vigna radiata
Map dataPlant mitochondrial supercomplex III2 IV from Vigna radiata.
Sample
  • Complex: Mitochondrial Respiratory Complex III2
Function / homology
Function and homology information


respiratory chain complex IV / : / : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport ...respiratory chain complex IV / : / : / : / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / ATP synthesis coupled electron transport / : / enzyme regulator activity / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / copper ion binding / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Predicted cytochrome c oxidase subunit VII / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily ...Cytochrome c oxidase subunit 5c / Protein of unknown function DUF1138 / Protein of unknown function (DUF1138) / Predicted cytochrome c oxidase subunit VII / Cytochrome b-c1 complex subunit 8, plants / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase, subunit VIb / : / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Cytochrome b-c1 complex, subunit 6 / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome c/quinol oxidase subunit II / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin
Similarity search - Domain/homology
Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein LOC106757297 / Complex III subunit 9 / Uncharacterized protein LOC106759053 / Probable mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 5b-2, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 6a, mitochondrial ...Cytochrome b-c1 complex subunit Rieske, mitochondrial / Uncharacterized protein LOC106757297 / Complex III subunit 9 / Uncharacterized protein LOC106759053 / Probable mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 5b-2, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 6a, mitochondrial / Cytochrome c oxidase subunit 5C / Uncharacterized protein LOC106772338 / Mitochondrial-processing peptidase subunit alpha / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 6b-1 / Cytochrome c1-2, heme protein, mitochondrial
Similarity search - Component
Biological speciesVigna radiata (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMaldonado M / Letts JA
CitationJournal: Elife / Year: 2021
Title: Atomic structures of respiratory complex III, complex IV, and supercomplex III-IV from vascular plants.
Authors: Maria Maldonado / Fei Guo / James A Letts /
Abstract: Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes ...Mitochondrial complex III (CIII) and complex IV (CIV), which can associate into a higher-order supercomplex (SC III+IV), play key roles in respiration. However, structures of these plant complexes remain unknown. We present atomic models of CIII, CIV, and SC III+IV from determined by single-particle cryoEM. The structures reveal plant-specific differences in the MPP domain of CIII and define the subunit composition of CIV. Conformational heterogeneity analysis of CIII revealed long-range, coordinated movements across the complex, as well as the motion of CIII's iron-sulfur head domain. The CIV structure suggests that, in plants, proton translocation does not occur via the H channel. The supercomplex interface differs significantly from that in yeast and bacteria in its interacting subunits, angle of approach and limited interactions in the mitochondrial matrix. These structures challenge long-standing assumptions about the plant complexes and generate new mechanistic hypotheses.
History
DepositionAug 12, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22449.png

Downloads & links

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Map

FileDownload / File: emd_22449.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlant mitochondrial supercomplex III2 IV from Vigna radiata.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.39135355 - 1.5675192
Average (Standard dev.)0.0055016847 (±0.05464203)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.5984 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.833199218750.833199218750.83319921875
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z426.598426.598426.598
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.3911.5680.006

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Supplemental data

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Mask #1

Fileemd_22449_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Plant mitochondrial supercomplex III2 IV from Vigna radiata....

Fileemd_22449_half_map_1.map
AnnotationPlant mitochondrial supercomplex III2 IV from Vigna radiata. Half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Plant mitochondrial supercomplex III2 IV from Vigna radiata....

Fileemd_22449_half_map_2.map
AnnotationPlant mitochondrial supercomplex III2 IV from Vigna radiata. Half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mitochondrial Respiratory Complex III2

EntireName: Mitochondrial Respiratory Complex III2
Components
  • Complex: Mitochondrial Respiratory Complex III2

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Supramolecule #1: Mitochondrial Respiratory Complex III2

SupramoleculeName: Mitochondrial Respiratory Complex III2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Vigna radiata (mung bean) / Tissue: hypocotyl / Organelle: mitochondria
Molecular weightTheoretical: 485 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
20.0 mMHEPES
150.0 mMsodium chlorideNaCl
1.0 mMEDTA
0.2 %digitonin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK III
DetailsThis sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 9816 / Average exposure time: 3.0 sec. / Average electron dose: 86.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 60010 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 150000000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: NONE / Details: Ab initio model generation
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28020
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: Stochastic gradient descent
Final angle assignmentType: OTHER / Software - Name: cryoSPARC / Details: Stochastic gradient descent
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

6q9e

,

6hu9

)
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 67 / Target criteria: correlation coefficient

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