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- EMDB-28798: Vigna radiata supercomplex I+III2 - bridgeless classes 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-28798
TitleVigna radiata supercomplex I+III2 - bridgeless classes 1
Map dataVigna radiata supercomplex I III2- bridgeless class1
Sample
  • Organelle or cellular component: Mitochondrial respiratory supercomplex I+III2
Keywordssupercomplex / respiration / ELECTRON TRANSPORT
Biological speciesVigna radiata (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsLetts JA / Maldonado M
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0022293 United States
CitationJournal: Nat Plants / Year: 2023
Title: Plant-specific features of respiratory supercomplex I + III from Vigna radiata.
Authors: M Maldonado / Z Fan / K M Abe / J A Letts /
Abstract: The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane ...The last steps of cellular respiration-an essential metabolic process in plants-are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I-V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III's mitochondrial processing peptidase domain and no participation of complex I's bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme's two arms, limiting large-scale conformational changes. Moreover, complex I's catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata, the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III. Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.
History
DepositionNov 5, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28798.png

Downloads & links

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Map

FileDownload / File: emd_28798.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVigna radiata supercomplex I III2- bridgeless class1
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 600 pix.
= 528. Å		0.88 Å/pix.
x 600 pix.
= 528. Å		0.88 Å/pix.
x 600 pix.
= 528. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.19116907 - 0.6756347
Average (Standard dev.)0.00030110727 (±0.018766593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28798_msk_1.map
Projections & Slices
AxesZYX

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Half map: Vigna radiata supercomplex I III2- bridgeless class1- half-mapA

Fileemd_28798_half_map_1.map
AnnotationVigna radiata supercomplex I III2- bridgeless class1- half-mapA
Projections & Slices
AxesZYX

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Half map: Vigna radiata supercomplex I III2- bridgeless class1- half-mapB

Fileemd_28798_half_map_2.map
AnnotationVigna radiata supercomplex I III2- bridgeless class1- half-mapB
Projections & Slices
AxesZYX

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Sample components

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Entire : Mitochondrial respiratory supercomplex I+III2

EntireName: Mitochondrial respiratory supercomplex I+III2
Components
  • Organelle or cellular component: Mitochondrial respiratory supercomplex I+III2

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Supramolecule #1: Mitochondrial respiratory supercomplex I+III2

SupramoleculeName: Mitochondrial respiratory supercomplex I+III2 / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Vigna radiata (mung bean)

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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

BufferpH: 7.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70363
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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