[English] 日本語
Yorodumi
- EMDB-10556: Cryo-EM map of human dihydrolipoamide succinyltransferase catalyt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10556
TitleCryo-EM map of human dihydrolipoamide succinyltransferase catalytic domain (DLST)
Map dataHuman dihydrolipoamide succinyltransferase (E2) component of the 2-oxoglutarate dehydrogenase complex
Sample
  • Complex: human dihydrolipoamide succinyltransferase (DLST)
    • Protein or peptide: human dihydrolipoamide succinyltransferase (DLST)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsBailey HJ / Bezerra GA / Foster W / Diaz Saez L / Yue WW
CitationJournal: To Be Published
Title: Cryo-EM map of human dihydrolipoamide succinyltransferase (DLST)
Authors: Bailey HJ / Bezerra GA / Foster W / Diaz Saez L / Yue WW
History
DepositionDec 18, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateFeb 19, 2020-
Current statusFeb 19, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10556.png

Downloads & links

-
Map

FileDownload / File: emd_10556.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman dihydrolipoamide succinyltransferase (E2) component of the 2-oxoglutarate dehydrogenase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 344 pix.
= 330.24 Å		0.96 Å/pix.
x 344 pix.
= 330.24 Å		0.96 Å/pix.
x 344 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.080750145 - 0.12508327
Average (Standard dev.)0.00045908339 (±0.0053014723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.960.960.96
M x/y/z344344344
origin x/y/z0.0000.0000.000
length x/y/z330.240330.240330.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS344344344
D min/max/mean-0.0810.1250.000

-
Supplemental data

-
Sample components

-
Entire : human dihydrolipoamide succinyltransferase (DLST)

EntireName: human dihydrolipoamide succinyltransferase (DLST)
Components
  • Complex: human dihydrolipoamide succinyltransferase (DLST)
    • Protein or peptide: human dihydrolipoamide succinyltransferase (DLST)

-
Supramolecule #1: human dihydrolipoamide succinyltransferase (DLST)

SupramoleculeName: human dihydrolipoamide succinyltransferase (DLST) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 1.059 MDa

-
Macromolecule #1: human dihydrolipoamide succinyltransferase (DLST)

MacromoleculeName: human dihydrolipoamide succinyltransferase (DLST) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGHHHHHHSS GVDLGTENLY FQSMDDLVTV KTPAFAESVT EGDVRWEKAV GDTVAEDEVV CEIETDKTSV QVPSPANGVI EALLVPDGGK VEGGTPLFTL RKTGAAPAKA KPAEAPAAAA PKAEPTAAAV PPPAAPIPTQ MPPVPSPSQP PSGKPVSAVK PTVAPPLAEP ...String:
MGHHHHHHSS GVDLGTENLY FQSMDDLVTV KTPAFAESVT EGDVRWEKAV GDTVAEDEVV CEIETDKTSV QVPSPANGVI EALLVPDGGK VEGGTPLFTL RKTGAAPAKA KPAEAPAAAA PKAEPTAAAV PPPAAPIPTQ MPPVPSPSQP PSGKPVSAVK PTVAPPLAEP GAGKGLRSEH REKMNRMRQR IAQRLKEAQN TCAMLTTFNE IDMSNIQEMR ARHKEAFLKK HNLKLGFMSA FVKASAFALQ EQPVVNAVID DTTKEVVYRD YIDISVAVAT PRGLVVPVIR NVEAMNFADI ERTITELGEK ARKNELAIED MDGGTFTISN GGVFGSLFGT PIINPPQSAI LGMHGIFDRP VAIGGKVEVR PMMYVALTYD HRLIDGREAV TFLRKIKAAV EDPRVLLLDL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
150.0 mMNaCl
0.5 mMTCEP
GridModel: Quantifoil R2/1 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Number grids imaged: 1 / Number real images: 619 / Average exposure time: 1.0 sec. / Average electron dose: 32.52 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal magnification: 150000

+
Image processing

Particle selectionNumber selected: 165739
CTF correctionSoftware - Name: CTFFIND
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 33072
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1 / Avg.num./class: 33072 / Software - Name: RELION
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://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