[English] 日本語
Yorodumi
- EMDB-4573: Full Elongator catalytic subcomplex Elp123 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4573
TitleFull Elongator catalytic subcomplex Elp123
Map dataPostprocessed map of the full Elongator catalytic subcomplex Elp123 from yeast at 4.5 A resolution.
Sample
  • Complex: Full Elongator catalytic subcomplex Elp123
    • Protein or peptide: Elongator complex protein 1, Elp1
    • Protein or peptide: Elongator complex protein 2, Elp2
    • Protein or peptide: Elongator complex protein 3, Elp3
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsDauden MI / Weis F
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research FoundationBR921/9-1 & Mu3173/2-1 Germany
CitationJournal: Sci Adv / Year: 2019
Title: Molecular basis of tRNA recognition by the Elongator complex.
Authors: Maria I Dauden / Marcin Jaciuk / Felix Weis / Ting-Yu Lin / Carolin Kleindienst / Nour El Hana Abbassi / Heena Khatter / Rościsław Krutyhołowa / Karin D Breunig / Jan Kosinski / Christoph ...Authors: Maria I Dauden / Marcin Jaciuk / Felix Weis / Ting-Yu Lin / Carolin Kleindienst / Nour El Hana Abbassi / Heena Khatter / Rościsław Krutyhołowa / Karin D Breunig / Jan Kosinski / Christoph W Müller / Sebastian Glatt /
Abstract: The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of ...The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo-electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer.
History
DepositionJan 29, 2019-
Header (metadata) releaseFeb 13, 2019-
Map releaseJul 17, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4573.png

Downloads & links

-
Map

FileDownload / File: emd_4573.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of the full Elongator catalytic subcomplex Elp123 from yeast at 4.5 A resolution.
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0314 / Movie #1: 0.0314
Minimum - Maximum-0.029659856 - 0.14864859
Average (Standard dev.)0.00031395676 (±0.003373668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 496.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z496.800496.800496.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0300.1490.000

-
Supplemental data

-
Half map: Half map of the full Elongator catalytic subcomplex...

Fileemd_4573_half_map_1.map
AnnotationHalf map of the full Elongator catalytic subcomplex Elp123 from yeast.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map of the full Elongator catalytic subcomplex...

Fileemd_4573_half_map_2.map
AnnotationHalf map of the full Elongator catalytic subcomplex Elp123 from yeast.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Full Elongator catalytic subcomplex Elp123

EntireName: Full Elongator catalytic subcomplex Elp123
Components
  • Complex: Full Elongator catalytic subcomplex Elp123
    • Protein or peptide: Elongator complex protein 1, Elp1
    • Protein or peptide: Elongator complex protein 2, Elp2
    • Protein or peptide: Elongator complex protein 3, Elp3

-
Supramolecule #1: Full Elongator catalytic subcomplex Elp123

SupramoleculeName: Full Elongator catalytic subcomplex Elp123 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The EM map corresponds to the full Elp123 complex, composed by two copies of Elp1, Elp2 and Elp3 forming a C2 symmetric complex.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 621 KDa

-
Macromolecule #1: Elongator complex protein 1, Elp1

MacromoleculeName: Elongator complex protein 1, Elp1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIG AIEVQQFMKD GSRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII T ATYDPVSL DPAETLIEIM GTIDNGIAAA QWSYDEETLA MVTKDRNVVV ...String:
MVEHDKSGSK RQELRSNMRN LITLNKGKFK PTASTAEGDE DDLSFTLLDS VFDTLSDSIT CVLGSTDIG AIEVQQFMKD GSRNVLASFN IQTFDDKLLS FVHFADINQL VFVFEQGDII T ATYDPVSL DPAETLIEIM GTIDNGIAAA QWSYDEETLA MVTKDRNVVV LSKLFEPISE YH LEVDDLK ISKHVTVGWG KKETQFRGKG ARAMEREALA SLKASGLVGN QLRDPTMPYM VDT GDVTAL DSHEITISWR GDCDYFAVSS VEEVPDEDDE TKSIKRRAFR VFSREGQLDS ASEP VTGME HQLSWKPQGS LIASIQRKTD LGEEDSVDVI FFERNGLRHG EFDTRLPLDE KVESV CWNS NSEALAVVLA NRIQLWTSKN YHWYLKQELY ASDISYVKWH PEKDFTLMFS DAGFIN IVD FAYKMAQGPT LEPFDNGTSL VVDGRTVNIT PLALANVPPP MYYRDFETPG NVLDVAC SF SNEIYAAINK DVLIFAAVPS IEEMKKGKHP SIVCEFPKSE FTSEVDSLRQ VAFINDSI V GVLLDTDNLS RIALLDIQDI TQPTLITIVE VYDKIVLLRS DFDYNHLVYE TRDGTVCQL DAEGQLMEIT KFPQLVRDFR VKRVHNTSAE DDDNWSAESS ELVAFGITNN GKLFANQVLL ASAVTSLEI TDSFLLFTTA QHNLQFVHLN STDFKPLPLV EEGVEDERVR AIERGSILVS V IPSKSSVV LQATRGNLET IYPRIMVLAE VRKNIMAKRY KEAFIVCRTH RINLDILHDY AP ELFIENL EVFINQIGRV DYLNLFISCL SEDDVTKTKY KETLYSGISK SFGMEPAPLT EMQ IYMKKK MFDPKTSKVN KICDAVLNVL LSNPEYKKKY LQTIITAYAS QNPQNLSAAL KLIS ELENS EEKDSCVTYL CFLQDVNVVY KSALSLYDVS LALLVAQKSQ MDPREYLPFL QELQD NEPL RRKFLIDDYL GNYEKALEHL SEIDKDGNVS EEVIDYVESH DLYKHGLALY RYDSEK QNV IYNIYAKHLS SNQMYTDAAV AYEMLGKLKE AMGAYQSAKR WREAMSIAVQ KFPEEVE SV AEELISSLTF EHRYVDAADI QLEYLDNVKE AVALYCKAYR YDIASLVAIK AKKDELLE E VVDPGLGEGF GIIAELLADC KGQINSQLRR LRELRAKKEE NPYAFYGQET EQADDVSVA PSETSTQESF FTRYTGKTGG TAKTGASRRT AKNKRREERK RARGKKGTIY EEEYLVQSVG RLIERLNQT KPDAVRVVEG LCRRNMREQA HQIQKNFVEV LDLLKANVKE IYSISEKDRE R VNENGEVY YIPEIPVPEI HDFPKSHIVD F

-
Macromolecule #2: Elongator complex protein 2, Elp2

MacromoleculeName: Elongator complex protein 2, Elp2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVP DSDFMVSASE DHHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV G CADGTISI WRQNIQNDEF GLAHEFTIKK GFFYPLCLSL SKVEEKKYLL ...String:
MVECITPEAI FIGANKQTQV SDIHKVKKIV AFGAGKTIAL WDPIEPNNKG VYATLKGHEA EVTCVRFVP DSDFMVSASE DHHVKIWKFT DYSHLQCIQT IQHYSKTIVA LSALPSLISV G CADGTISI WRQNIQNDEF GLAHEFTIKK GFFYPLCLSL SKVEEKKYLL AIGGTNVNVF IA SFILSDS GIEKCRVVAE LEGHEDWVKS LAFRHQETPG DYLLCSGSQD RYIRLWRIRI NDL IDDSEE DSKKLTLLSN KQYKFQIDDE LRVGINFEAL IMGHDDWISS LQWHESRLQL LAAT ADTSL MVWEPDETSG IWVCSLRLGE MSSKGASTAT GSSGGFWSCL WFTHERMDFF LTNGK TGSW RMWATKDNII CDQRLGISGA TKDVTDIAWS PSGEYLLATS LDQTTRLFAP WIYDAS GRK REIATWHEFS RPQIHGYDMI CVETVTDTRF VSGGDEKILR SFDLPKGVAG MLQKFVG IQ FEEKSEMPDS ATVPVLGLSN KAGEDDANED DEEEEGGNKE TPDITDPLSL LECPPMED Q LQRHLLWPEV EKLYGHGFEI TCLDISPDQK LIASACRSNN VQNAVIRIFS TENWLEIKP ALPFHSLTIT RLKFSKDGKF LLSVCRDRKW ALWERNMEDN TFELRFKNEK PHTRIIWDAD WAPLEFGNV FVTASRDKTV KVWRHQKEPA DDYVLEASIK HTKAVTAISI HDSMIREKIL I SVGLENGE IYLYSYTLGK FELITQLNED ITPADKITRL RWSHLKRNGK LFLGVGSSDL ST RIYSLAY E

-
Macromolecule #3: Elongator complex protein 3, Elp3

MacromoleculeName: Elongator complex protein 3, Elp3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDI INSIPDQYKK YLLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV Y CPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPYEQAR GRVEQLKQLG ...String:
MARHGKGPKT NKKKLAPEKE RFIQCCADIT LELTDSLTSG TTREINLNGL ITKYSKKYKL KQQPRLTDI INSIPDQYKK YLLPKLKAKP VRTASGIAVV AVMCKPHRCP HIAYTGNICV Y CPGGPDSD FEYSTQSYTG YEPTSMRAIR ARYDPYEQAR GRVEQLKQLG HSIDKVEYVL MG GTFMSLP KEYREDFIVK LHNALSGFNG NDIDEAILYS QQSLTKCVGI TIETRPDYCT QTH LDDMLK YGCTRLEIGV QSLYEDVARD TNRGHTVRSV CETFAVSKDA GYKVVSHMMP DLPN VGMER DIEQFKEYFE NPDFRTDGLK IYPTLVIRGT GLYELWKTGR YKSYSANALV DLVAR ILAL VPPWTRIYRV QRDIPMPLVT SGVDNGNLRE LALARMKDLG TTCRDVRTRE VGIQEV HHK VQPDQVELIR RDYYANGGWE TFLSYEDPKK DILIGLLRLR KASKKYTYRK EFTSQRT SI VRELHVYGSV VPLHSRDPRK FQHQGFGTLL MEEAERIAKE EHGSEKISVI SGVGVRNY Y GKLGYELDGP YMSKRI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMHepesHepes
125.0 mMNaClSodium chlorideSodium chloride
50.0 mMNaFSodium fluoride
0.1 mMNa3VO4Sodium vanadate
5.0 mMC2H6OSbeta-mercaptoethanol2-Mercaptoethanol
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Details: Pelco EasyGlow glow discharger
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 2.5 ul of sample, blotting parameters: wait time 15 s, blot force 5, blot time 5-8 s..
DetailsThe sample was cross-linked with 0.01% glutaraldehyde, quenched and then plunged.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
DetailsGatan Quantum energy filter and a K2 Summit direct detector
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 4614 / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1000000
Details: Initially 8563 particles were manually selected using EMAN2 boxer swarm tool, and used as 2D templates for the autopicking procedure in relion, that yielded 1 million particles.
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

4151


Details: The initial model was low pass filtered to 60 A.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 5 / Avg.num./class: 98000 / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 45236
DetailsThe detector was operated in super resolution mode.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5m2n

chain_id: B

5cqs

chain_id: A, D
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