[English] 日本語
Yorodumi
- EMDB-4151: S.cerevisiae Elp123 sub-complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4151
TitleS.cerevisiae Elp123 sub-complex
Map dataNegative staining reconstruction of the S.cerevisiae Elp123 sub-complex
Sample
  • Complex: S.cerevisiae Elp123 sub-complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsDauden MI / Kosinski J / Kolaj-Robin O / Desfosses A / Ori A / Faux C / Hoffmann NA / Onuma OF / Breuring KD / Beck M ...Dauden MI / Kosinski J / Kolaj-Robin O / Desfosses A / Ori A / Faux C / Hoffmann NA / Onuma OF / Breuring KD / Beck M / Sachse C / Seraphin B / Glatt S / Mueller CW
CitationJournal: EMBO Rep / Year: 2017
Title: Architecture of the yeast Elongator complex.
Authors: Maria I Dauden / Jan Kosinski / Olga Kolaj-Robin / Ambroise Desfosses / Alessandro Ori / Celine Faux / Niklas A Hoffmann / Osita F Onuma / Karin D Breunig / Martin Beck / Carsten Sachse / ...Authors: Maria I Dauden / Jan Kosinski / Olga Kolaj-Robin / Ambroise Desfosses / Alessandro Ori / Celine Faux / Niklas A Hoffmann / Osita F Onuma / Karin D Breunig / Martin Beck / Carsten Sachse / Bertrand Séraphin / Sebastian Glatt / Christoph W Müller /
Abstract: The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is ...The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.
History
DepositionOct 17, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseDec 21, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4151.png

Downloads & links

-
Map

FileDownload / File: emd_4151.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative staining reconstruction of the S.cerevisiae Elp123 sub-complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 224 pix.
= 492.8 Å		2.2 Å/pix.
x 224 pix.
= 492.8 Å		2.2 Å/pix.
x 224 pix.
= 492.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.030151892 - 0.10843984
Average (Standard dev.)0.000017414928 (±0.0055633634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 492.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z492.800492.800492.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.0300.1080.000

-
Supplemental data

-
Sample components

-
Entire : S.cerevisiae Elp123 sub-complex

EntireName: S.cerevisiae Elp123 sub-complex
Components
  • Complex: S.cerevisiae Elp123 sub-complex

-
Supramolecule #1: S.cerevisiae Elp123 sub-complex

SupramoleculeName: S.cerevisiae Elp123 sub-complex / type: complex / ID: 1 / Parent: 0
Details: Composed of two copies of its three subunits: Elp1, Elp2 and Elp3.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BS1173
Molecular weightTheoretical: 621 KDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.035 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES buffer
125.0 mMNaClSodium chloride
5.0 mMC2H6OS2-mercaptoethanol
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: 3.5 ul aliquots of freshly purified Elp123 complex were applied to glow discharged carbon copper-collodion (Sigma) grids for 2 min and stained with a 1% uranyl acetate solution (w/v)
GridModel: Plano D-35578 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Details: 0.45mBar, 20mA

-
Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 216 / Average electron dose: 16.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.3 mm / Nominal magnification: 49000

+
Image processing

Particle selectionNumber selected: 50034
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: RANDOM CONICAL TILT / Random conical tilt - Number images: 120 / Random conical tilt - Tilt angle: 55 degrees
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 2051
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: Xmipp
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 2 / Avg.num./class: 3200 / Software - Name: RELION (ver. 1.4)
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