[English] 日本語
Yorodumi
- EMDB-61082: The map of pyruvate dehydrogenase E1 bound to the peripheral subu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61082
TitleThe map of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain and lipoyl domain of E2
Map data
Sample
  • Complex: Conformation of E1 with PSBD and LD in E2 components of pyruvate dehydrogenase complex
Keywordslipoyl domains / pyruvate dehydrogenase / dihydrolipoyl transacetylase / STRUCTURAL PROTEIN / TRANSFERASE
Biological speciesSus scrofa (pig)
Methodsubtomogram averaging / cryo EM / Resolution: 8.2 Å
AuthorsWang C / Zhang X / Chang Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0507700 China
National Natural Science Foundation of China (NSFC)32200980 China
CitationJournal: Nat Commun / Year: 2025
Title: Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis.
Authors: Wang C / Ma C / Xu Y / Chang S / Wu H / Yan C / Chen J / Wu Y / An S / Xu J / Han Q / Jiang Y / Jiang Z / Chu X / Gao H / Zhang X / Chang Y
History
DepositionAug 5, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_61082.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 3 Å
Density
Contour LevelBy AUTHOR: 0.0028
Minimum - Maximum-0.0034782765 - 0.009991685
Average (Standard dev.)0.0000207837 (±0.0005525887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Conformation of E1 with PSBD and LD in E2 components of pyruvate ...

EntireName: Conformation of E1 with PSBD and LD in E2 components of pyruvate dehydrogenase complex
Components
  • Complex: Conformation of E1 with PSBD and LD in E2 components of pyruvate dehydrogenase complex

-
Supramolecule #1: Conformation of E1 with PSBD and LD in E2 components of pyruvate ...

SupramoleculeName: Conformation of E1 with PSBD and LD in E2 components of pyruvate dehydrogenase complex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 378
ExtractionNumber tomograms: 378 / Number images used: 37235
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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