[English] 日本語
Yorodumi
- EMDB-1151: Electron cryotomography of the E. coli pyruvate and 2-oxoglutarat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1151
TitleElectron cryotomography of the E. coli pyruvate and 2-oxoglutarate dehydrogenase complexes.
Map dataVolume of an extracted E. coli pyruvate dehydrogenase multienzyme complex particle from a dual-tilt tomogram.
Sample
  • Sample: Unengineered E. coli Pyruvate Dehydrogenase Multienzyme Complex
  • Protein or peptide: E2p octahedral core
  • Protein or peptide: E1p
  • Protein or peptide: E3
Function / homologyPyruvate dehydrogenase E1 component / Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / Dihydrolipoamide dehydrogenase
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsubtomogram averaging / cryo EM / Resolution: 55.0 Å
AuthorsMurphy GE / Jensen GJ
CitationJournal: Structure / Year: 2005
Title: Electron cryotomography of the E. coli pyruvate and 2-oxoglutarate dehydrogenase complexes.
Authors: Gavin E Murphy / Grant J Jensen /
Abstract: The E. coli pyruvate and 2-oxoglutarate dehydrogenases are two closely related, large complexes that exemplify a growing number of multiprotein "machines" whose domains have been studied extensively ...The E. coli pyruvate and 2-oxoglutarate dehydrogenases are two closely related, large complexes that exemplify a growing number of multiprotein "machines" whose domains have been studied extensively and modeled in atomic detail, but whose quaternary structures have remained unclear for lack of an effective imaging technology. Here, electron cryotomography was used to show that the E1 and E3 subunits of these complexes are flexibly tethered approximately 11 nm away from the E2 core. This result demonstrates unambiguously that electron cryotomography can reveal the relative positions of features as small as 80 kDa in individual complexes, elucidating quaternary structure and conformational flexibility.
History
DepositionAug 13, 2005-
Header (metadata) releaseAug 16, 2005-
Map releaseFeb 3, 2006-
UpdateSep 2, 2011-
Current statusSep 2, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 23
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 23
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1151.gif

Downloads & links

-
Map

FileDownload / File: emd_1151.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationVolume of an extracted E. coli pyruvate dehydrogenase multienzyme complex particle from a dual-tilt tomogram.
Voxel sizeX=Y=Z: 8.2 Å
Density
Contour LevelBy EMDB: 20.0 / Movie #1: 23
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-24.177199999999999 (±16.0382)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 656 Å
α=β=γ: 90 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z8.28.28.2
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z656.000656.000656.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-69
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-128.000127.000-24.177

-
Supplemental data

-
Sample components

-
Entire : Unengineered E. coli Pyruvate Dehydrogenase Multienzyme Complex

EntireName: Unengineered E. coli Pyruvate Dehydrogenase Multienzyme Complex
Components
  • Sample: Unengineered E. coli Pyruvate Dehydrogenase Multienzyme Complex
  • Protein or peptide: E2p octahedral core
  • Protein or peptide: E1p
  • Protein or peptide: E3

-
Supramolecule #1000: Unengineered E. coli Pyruvate Dehydrogenase Multienzyme Complex

SupramoleculeName: Unengineered E. coli Pyruvate Dehydrogenase Multienzyme Complex
type: sample / ID: 1000
Details: The sample was thawed from storage at -80 degrees Celcius before being loaded onto the grid.
Oligomeric state: Up to 24 pyruvate dehydrogenase E1p and dihydrolipoamide dehydrogenase E3 dimers together bind to the 24 dihydrolipoamide acetyltransferase E2p octahedral core.
Number unique components: 3
Molecular weightTheoretical: 5.6 MDa

-
Macromolecule #1: E2p octahedral core

MacromoleculeName: E2p octahedral core / type: protein_or_peptide / ID: 1 / Name.synonym: dihydrolipoamide acetyltransferase
Details: 24 arranged as cube; See Wagenknecht, T. et al., JSB 109:70-77 (1992).
Number of copies: 24 / Oligomeric state: 24mer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli / Location in cell: cytoplasm
Molecular weightExperimental: 1.6 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceInterPro: Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex

-
Macromolecule #2: E1p

MacromoleculeName: E1p / type: protein_or_peptide / ID: 2 / Name.synonym: pyruvate dehydrogenase
Details: Up to 24 of these; See Wagenknecht, T. et al., JSB 109:70-77 (1992).
Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli / Location in cell: cytoplasm
Molecular weightExperimental: 200 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceInterPro: Pyruvate dehydrogenase E1 component

-
Macromolecule #3: E3

MacromoleculeName: E3 / type: protein_or_peptide / ID: 3 / Name.synonym: dihydrolipoamide dehydrogenase
Details: Up to 24 of these; See Wagenknecht, T. et al., JSB 109:70-77 (1992).
Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli / Location in cell: Cytoplasm
Molecular weightExperimental: 100 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceInterPro: Dihydrolipoamide dehydrogenase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7 / Details: 20 mM Potassium Phosphate
GridDetails: R 1.5/1.3 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER
Details: Vitrification instrument: Vitrobot. Sample was at 22 C in air before plunging.
Method: Blot for 3.5 seconds with an offset of -3 before plunging.

-
Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 10.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 27500
Specialist opticsEnergy filter - Name: GIF 3000 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: FEI Polara / Specimen holder model: GATAN HELIUM / Tilt series - Axis1 - Min angle: -63 ° / Tilt series - Axis1 - Max angle: 66 °
TemperatureMin: 82 K / Max: 82 K / Average: 82 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateAug 24, 2004
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 110 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 55.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD
Details: The individual, orthogonal tomograms were filtered at their first CTF zero and then merged.
DetailsDual-axis tilt series, with 44 sections on one axis, and 45 on the other. Average number of tilts used in the 3D reconstructions: 89. Average tomographic tilt angle increment: 3.

-
Atomic model buiding 1

Initial model(PDB ID:

1l8a

,

1dpc

,

1ebd

)
DetailsThe octameric E2p core (1DPC) was fit into the core density using bfind from the Bsoft package. Up to 24 E1p (1L8A) and E3 (1EBD) dimers were fit into the peripheral density manually using Amira.
RefinementProtocol: 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