[English] 日本語
Yorodumi
- EMDB-15635: Cryo-EM structure of yeast Elp456 subcomplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15635
TitleCryo-EM structure of yeast Elp456 subcomplex
Map data
Sample
  • Complex: Yeast Elp456 subcomplex
    • Protein or peptide: Elongator complex protein 4
    • Protein or peptide: Elongator complex protein 5
    • Protein or peptide: Elongator complex protein 6
Keywordswobble uridine modification / TRANSLATION
Function / homology
Function and homology information


elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / peroxisome / regulation of translation / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding ...elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / peroxisome / regulation of translation / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Elongator complex protein 4 / Elongator complex protein 6 / Elongator complex protein 5 / PAXNEB protein / Elongator subunit Iki1 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Elongator complex protein 5 / Elongator complex protein 4 / Elongator complex protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsJaciuk M / Scherf D / Kaszuba K / Gaik M / Koscielniak A / Krutyholowa R / Rawski M / Indyka P / Biela A / Dobosz D ...Jaciuk M / Scherf D / Kaszuba K / Gaik M / Koscielniak A / Krutyholowa R / Rawski M / Indyka P / Biela A / Dobosz D / Lin T-Y / Abbassi N / Hammermeister A / Chramiec-Glabik A / Kosinski J / Schaffrath R / Glatt S
Funding support Poland, European Union, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2018/31/B/NZ1/03559 Poland
European Research Council (ERC)101001394European Union
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Cryo-EM structure of the fully assembled Elongator complex.
Authors: Marcin Jaciuk / David Scherf / Karol Kaszuba / Monika Gaik / Alexander Rau / Anna Kościelniak / Rościsław Krutyhołowa / Michał Rawski / Paulina Indyka / Andrea Graziadei / Andrzej ...Authors: Marcin Jaciuk / David Scherf / Karol Kaszuba / Monika Gaik / Alexander Rau / Anna Kościelniak / Rościsław Krutyhołowa / Michał Rawski / Paulina Indyka / Andrea Graziadei / Andrzej Chramiec-Głąbik / Anna Biela / Dominika Dobosz / Ting-Yu Lin / Nour-El-Hana Abbassi / Alexander Hammermeister / Juri Rappsilber / Jan Kosinski / Raffael Schaffrath / Sebastian Glatt /
Abstract: Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition ...Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes.
History
DepositionAug 22, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15635.png

Downloads & links

-
Map

FileDownload / File: emd_15635.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242
Minimum - Maximum-0.035762765 - 0.07653746
Average (Standard dev.)0.00009877364 (±0.0017283901)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_15635_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15635_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Yeast Elp456 subcomplex

EntireName: Yeast Elp456 subcomplex
Components
  • Complex: Yeast Elp456 subcomplex
    • Protein or peptide: Elongator complex protein 4
    • Protein or peptide: Elongator complex protein 5
    • Protein or peptide: Elongator complex protein 6

-
Supramolecule #1: Yeast Elp456 subcomplex

SupramoleculeName: Yeast Elp456 subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 233.8 KDa

-
Macromolecule #1: Elongator complex protein 4

MacromoleculeName: Elongator complex protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 51.232469 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSFRKRGEIL NDRGSGLRGP LLRGPPRTSS TPLRTGNRRA PGNVPLSDTT ARLKKLNIAD ESKTKMGLDS SHVGVRPSPA TSQPTTSTG SADLDSILGH MGLPLGNSVL VEEQSTTEFH SILGKLFAAQ GIVHNRISDS SADKTRNGDT HVIVLSLNQM F AKELPGIY ...String:
MSFRKRGEIL NDRGSGLRGP LLRGPPRTSS TPLRTGNRRA PGNVPLSDTT ARLKKLNIAD ESKTKMGLDS SHVGVRPSPA TSQPTTSTG SADLDSILGH MGLPLGNSVL VEEQSTTEFH SILGKLFAAQ GIVHNRISDS SADKTRNGDT HVIVLSLNQM F AKELPGIY KGSRKQMKKN LISEEESKVT VQNLNETQRS TPSRYKDLKI AWKYKLADEK RLGSPDRDDI QQNSEYKDYN HQ FDITTRL MPAPIASELT FIAPTQPVST ILSQIEQTIK RNDKKLIRIV IPSLLHPAMY PPKMFESSEI IGLMHGVRSL VKK YYERVV LFASISIDII TPPLLVLLRN MFDSVINLEP FNQEMTEFLE RVYKSQPGKI QHGLVHILKL PVFTDRGEMR VLKS EWAFK NGRKKFEIEQ WGIPVDDAEG SAASEQSHSH SHSDEISHNI PAKKTKISLD Y

UniProtKB: Elongator complex protein 4

-
Macromolecule #2: Elongator complex protein 5

MacromoleculeName: Elongator complex protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 35.252496 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASSSHNPVI LLKRILSLTE SSPFILCLDS IAQTSYKLIQ EFVHQSKSKG NEYPIVYISF ETVNKPSYCT QFIDATQMDF VHLVKQIIS YLPAATATQA KKHMVIIDSL NYISTEYITR FLSEIASPHC TMVATYHKDI KDENRTVIPD WNNNYPDKLT L LQFMATTI ...String:
MASSSHNPVI LLKRILSLTE SSPFILCLDS IAQTSYKLIQ EFVHQSKSKG NEYPIVYISF ETVNKPSYCT QFIDATQMDF VHLVKQIIS YLPAATATQA KKHMVIIDSL NYISTEYITR FLSEIASPHC TMVATYHKDI KDENRTVIPD WNNNYPDKLT L LQFMATTI VDIDVVLTGT LDTEEVSELL NEFRIPRGLN NDIFQLRLVN KRKSGRSLEY DFIVNSNTHE YELLSTTKQE EE SSSNGLE TPEMLQGLTT FNLGTSNKQK LAKDQVALPF LEAQSFGQGG AIVYEYEKDD DYDEEDPYED PF

UniProtKB: Elongator complex protein 5

-
Macromolecule #3: Elongator complex protein 6

MacromoleculeName: Elongator complex protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.602611 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGSVQRQDLV LFSDQSVLPA HFFQDSNSHN LFFITHQSCT QPLWMINALV ETHVLGSPSS LNESSSSMLP SSTRSHAVLA SFIHEQNYF TNSLNKLKIP SNNYNVLDFL SDFIVNNIHN KPRDKILSDV LAKFSAAIQN NPTDTIVIIE QPELLLSLVS G LTCSELNN ...String:
MGSVQRQDLV LFSDQSVLPA HFFQDSNSHN LFFITHQSCT QPLWMINALV ETHVLGSPSS LNESSSSMLP SSTRSHAVLA SFIHEQNYF TNSLNKLKIP SNNYNVLDFL SDFIVNNIHN KPRDKILSDV LAKFSAAIQN NPTDTIVIIE QPELLLSLVS G LTCSELNN KFITPLLRQC KVLIIVSNSD IFNIDEYDAS VHSSNLQNFY KSSFIKSMIN LNLNPLKTGF AKDVTGSLHV CR GGAPIAT SNTSLHVVEN EYLYLNEKES TKLFYR

UniProtKB: Elongator complex protein 6

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMHEPESHEPES
3.0 mMDithiothreitolDithiothreitol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 15 s wait time, blot force 5, 5 s blot time.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4716 / Average exposure time: 1.82 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Details20 eV slit, fully tuned before the experiment
Particle selectionNumber selected: 364424
Details: given number of particles is after TOPAZ picking and 2D cleaning
Startup modelType of model: INSILICO MODEL
In silico model: SWISS-MODEL generated full length Elp456 based on 4A8J structure
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Software - details: Postprocessing
Details: Given global resolution estimation for post-process sharpened map
Number images used: 128593
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0) / Software - details: Ab-Initio Reconstruction / Details: Ab-Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) / Software - details: 3D auto-refine / Details: 3D auto-refine
Final 3D classificationNumber classes: 5 / Avg.num./class: 12500 / Software - Name: RELION (ver. 3.1) / Software - details: masked 3D classification
Details: masked 3D classification with two classes of nice Elp456 density, each approx. 65k ptcls; and 3 remaining classes, each approx. 33k ptcls
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4a8j


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsAfter initial rigid body fit, further fitting was done using NAMDINATOR
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8at6:
Cryo-EM structure of yeast Elp456 subcomplex

+
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