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- EMDB-16153: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-16153
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Complete consensus)
Map dataConsensus map
Sample
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete consensus)
KeywordsPlant / Mitochondria / Complex / MEMBRANE PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsKlusch N / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
History
DepositionNov 17, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16153.png

Downloads & links

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Map

FileDownload / File: emd_16153.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map
Voxel sizeX=Y=Z: 0.573 Å
Density
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.1075296 - 3.1045268
Average (Standard dev.)0.005021919 (±0.06629795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 429.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Consensus half map

Fileemd_16153_half_map_1.map
AnnotationConsensus half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus half map

Fileemd_16153_half_map_2.map
AnnotationConsensus half map
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 Arabidopsis thaliana I+III2 supercomplex (Complete ...

EntireName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete consensus)
Components
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete consensus)

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Supramolecule #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete ...

SupramoleculeName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Complete consensus)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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

Concentration0.18 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1215138
Startup modelType of model: EMDB MAP
EMDB ID:

11878

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.0.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.0.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.0.2) / Number images used: 213993
FSC plot (resolution estimation)

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