[English] 日本語
Yorodumi
- EMDB-11269: E2 core of the fungal Pyruvate dehydrogenase complex with absent ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11269
TitleE2 core of the fungal Pyruvate dehydrogenase complex with absent periphery, structured core and empty interior.
Map dataFungal PDC (N. crassa). Recombinant preparation-E2. Enforced symmetry: I2. Periphery (E2 only) is flexible/oversym. Core is structured. Interior is empty.
Sample
  • Complex: E2 core of the fungal Pyruvate dehydrogenase complex with absent periphery, structured core and empty interior.
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsForsberg BO / Lindahl E / Aibara S / Howard RJ / Mortezaei N
Funding support Sweden, European Union, 5 items
OrganizationGrant numberCountry
Swedish Research Council2015-04107 Sweden
European Research Council (ERC)ERC-2018-StG-805230European Union
Swedish Research Council2017-04641 Sweden
Knut and Alice Wallenberg Foundation2018.0080 Sweden
European Research Council (ERC)bioexcel-823830European Union
CitationJournal: Nat Commun / Year: 2020
Title: Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex.
Authors: B O Forsberg / S Aibara / R J Howard / N Mortezaei / E Lindahl /
Abstract: The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) ...The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.
History
DepositionJun 30, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateDec 16, 2020-
Current statusDec 16, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.044
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11269.png

Downloads & links

-
Map

FileDownload / File: emd_11269.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFungal PDC (N. crassa). Recombinant preparation-E2. Enforced symmetry: I2. Periphery (E2 only) is flexible/oversym. Core is structured. Interior is empty.
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy AUTHOR: 0.044 / Movie #1: 0.044
Minimum - Maximum-0.07883227 - 0.13346662
Average (Standard dev.)0.0004900665 (±0.0057209013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 472.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z472.320472.320472.320
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0790.1330.000

-
Supplemental data

-
Half map: Half-map 1. Fungal PDC (N. crassa). Recombinant preparation-E2....

Fileemd_11269_half_map_1.map
AnnotationHalf-map 1. Fungal PDC (N. crassa). Recombinant preparation-E2. Enforced symmetry: I2. Periphery (E2 only) is flexible/oversym. Core is structured. Interior is empty.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2. Fungal PDC (N. crassa). Recombinant preparation-E2....

Fileemd_11269_half_map_2.map
AnnotationHalf-map 2. Fungal PDC (N. crassa). Recombinant preparation-E2. Enforced symmetry: I2. Periphery (E2 only) is flexible/oversym. Core is structured. Interior is empty.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : E2 core of the fungal Pyruvate dehydrogenase complex with absent ...

EntireName: E2 core of the fungal Pyruvate dehydrogenase complex with absent periphery, structured core and empty interior.
Components
  • Complex: E2 core of the fungal Pyruvate dehydrogenase complex with absent periphery, structured core and empty interior.

-
Supramolecule #1: E2 core of the fungal Pyruvate dehydrogenase complex with absent ...

SupramoleculeName: E2 core of the fungal Pyruvate dehydrogenase complex with absent periphery, structured core and empty interior.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Neurospora crassa (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 33.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7347
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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