[English] 日本語
Yorodumi
- EMDB-29203: V. radiata respiratory supercomplex I+III2 bridgeless class 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-29203
TitleV. radiata respiratory supercomplex I+III2 bridgeless class 4
Map dataBridgeless supercomplex I III2 class 4_mask
Sample
  • Complex: Vigna radiata supercomplex I+III2 (full bridge)
Biological speciesVigna radiata (mung bean)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsMaldonado M / Letts JA
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
DepositionDec 15, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_29203.png

Downloads & links

-
Map

FileDownload / File: emd_29203.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBridgeless supercomplex I III2 class 4_mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.08328481 - 0.6343897
Average (Standard dev.)0.00027689003 (±0.016722335)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_29203_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Bridgeless supercomplex I III2 class 4 half map A

Fileemd_29203_half_map_1.map
AnnotationBridgeless supercomplex I III2 class 4_half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Bridgeless supercomplex I III2 class 4 half map B

Fileemd_29203_half_map_2.map
AnnotationBridgeless supercomplex I III2 class 4_half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vigna radiata supercomplex I+III2 (full bridge)

EntireName: Vigna radiata supercomplex I+III2 (full bridge)
Components
  • Complex: Vigna radiata supercomplex I+III2 (full bridge)

-
Supramolecule #1: Vigna radiata supercomplex I+III2 (full bridge)

SupramoleculeName: Vigna radiata supercomplex I+III2 (full bridge) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#59
Details: Higher-order assembly between respiratory complex I and complex III2
Source (natural)Organism: Vigna radiata (mung bean)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.55 mg/mL
BufferpH: 7.7
Details: 0.2% digitonin, 30 mM HEPES pH 7.7, 150 mM potassium acetate, 1 mM EDTA, 0.002% PMSF
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP / Details: 4 ul, 20 seconds pre-blot, blot 4 seconds.
DetailsDigitonin-extracted, amphipol (A8-35)stabilized

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 25712 / 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
Sample stageCooling holder cryogen: NITROGEN

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 18173
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more