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- EMDB-16159: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-16159
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (Conformation 1 CIII)
Map dataFocused map
Sample
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Conformation 1 CIII).
KeywordsPlant / Mitochondria / Complex / MEMBRANE PROTEIN
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsKlusch N / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the respiratory I + III2 supercomplex from Arabidopsis thaliana at 2 A resolution
Authors: Klusch N / Dreimann M / Senkler J / Rugen N / Kuehlbrandt W / Braun HP
History
DepositionJan 18, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16159.png

Downloads & links

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Map

FileDownload / File: emd_16159.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 750 pix.
= 429.75 Å		0.57 Å/pix.
x 750 pix.
= 429.75 Å		0.57 Å/pix.
x 750 pix.
= 429.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.029744841 - 0.06676198
Average (Standard dev.)0.000054515534 (±0.0009310307)
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: Focused half map

Fileemd_16159_half_map_1.map
AnnotationFocused half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused half map

Fileemd_16159_half_map_2.map
AnnotationFocused 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 (Conformat...

EntireName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Conformation 1 CIII).
Components
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Conformation 1 CIII).

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

SupramoleculeName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (Conformation 1 CIII).
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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 61200
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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