[English] 日本語
Yorodumi
- EMDB-16841: S.cerevisiae THO complex from endogenous nuclear mRNPs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16841
TitleS.cerevisiae THO complex from endogenous nuclear mRNPs
Map datadimer masked map
Sample
  • Complex: THO complex dimer
    • Protein or peptide: THO complex subunit 2
    • Protein or peptide: THO complex subunit HPR1
    • Protein or peptide: THO complex subunit MFT1
    • Protein or peptide: Protein TEX1
    • Protein or peptide: THO complex subunit THP2
KeywordsComplex / Nuclear / Dimer / NUCLEAR PROTEIN
Function / homology
Function and homology information


nucleoplasmic THO complex / THO complex part of transcription export complex / positive regulation of transcription elongation by RNA polymerase I / transcription export complex / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / stress granule assembly ...nucleoplasmic THO complex / THO complex part of transcription export complex / positive regulation of transcription elongation by RNA polymerase I / transcription export complex / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / stress granule assembly / transcription elongation by RNA polymerase II / mRNA processing / DNA recombination / nucleic acid binding / chromosome, telomeric region / molecular adaptor activity / mRNA binding / nucleus
Similarity search - Function
THO complex subunit Thp2 / Tho complex subunit THP2 / TREX component Tex1/THOC3 / THO complex subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 / Transcription factor/nuclear export subunit protein 2 ...THO complex subunit Thp2 / Tho complex subunit THP2 / TREX component Tex1/THOC3 / THO complex subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 / Transcription factor/nuclear export subunit protein 2 / Transcription- and export-related complex subunit / THO complex subunit 2 N-terminus / THO complex, subunit THOC1 / THO complex subunit 1 transcription elongation factor / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
THO complex subunit THP2 / THO complex subunit HPR1 / THO complex subunit MFT1 / THO complex subunit 2 / Protein TEX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae BY4741 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsBonneau F / Schaefer IB / Conti E
Funding supportEuropean Union, Germany, Denmark, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
CitationJournal: Genes Dev / Year: 2023
Title: Nuclear mRNPs are compact particles packaged with a network of proteins promoting RNA-RNA interactions.
Authors: Fabien Bonneau / Jérôme Basquin / Barbara Steigenberger / Tillman Schäfer / Ingmar B Schäfer / Elena Conti /
Abstract: Messenger RNAs (mRNAs) are at the center of the central dogma of molecular biology. In eukaryotic cells, these long ribonucleic acid polymers do not exist as naked transcripts; rather, they associate ...Messenger RNAs (mRNAs) are at the center of the central dogma of molecular biology. In eukaryotic cells, these long ribonucleic acid polymers do not exist as naked transcripts; rather, they associate with mRNA-binding proteins to form messenger ribonucleoprotein (mRNP) complexes. Recently, global proteomic and transcriptomic studies have provided comprehensive inventories of mRNP components. However, knowledge of the molecular features of distinct mRNP populations has remained elusive. We purified endogenous nuclear mRNPs from by harnessing the mRNP biogenesis factors THO and Sub2 in biochemical procedures optimized to preserve the integrity of these transient ribonucleoprotein assemblies. We found that these mRNPs are compact particles that contain multiple copies of Yra1, an essential protein with RNA-annealing properties. To investigate their molecular and architectural organization, we used a combination of proteomics, RNA sequencing, cryo-electron microscopy, cross-linking mass spectrometry, structural models, and biochemical assays. Our findings indicate that yeast nuclear mRNPs are packaged around an intricate network of interconnected proteins capable of promoting RNA-RNA interactions via their positively charged intrinsically disordered regions. The evolutionary conservation of the major mRNA-packaging factor (yeast Yra1 and Aly/REF in metazoans) points toward a general paradigm governing nuclear mRNP packaging.
History
DepositionMar 13, 2023-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16841.png

Downloads & links

-
Map

FileDownload / File: emd_16841.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdimer masked map
Voxel sizeX=Y=Z: 1.885 Å
Density
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.19695333 - 0.71959984
Average (Standard dev.)-0.0006018533 (±0.028224897)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 610.74 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16841_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: dimer half map A

Fileemd_16841_half_map_1.map
Annotationdimer half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: dimer half map B

Fileemd_16841_half_map_2.map
Annotationdimer half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : THO complex dimer

EntireName: THO complex dimer
Components
  • Complex: THO complex dimer
    • Protein or peptide: THO complex subunit 2
    • Protein or peptide: THO complex subunit HPR1
    • Protein or peptide: THO complex subunit MFT1
    • Protein or peptide: Protein TEX1
    • Protein or peptide: THO complex subunit THP2

-
Supramolecule #1: THO complex dimer

SupramoleculeName: THO complex dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: From nuclear mRNPs isolated by bi-molecular affinity purification using Sub2 and Hpr1 as baits, then treated with Benzonase.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BY4741

-
Macromolecule #1: THO complex subunit 2

MacromoleculeName: THO complex subunit 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MAEQTLLSKL NALSQKVIPP ASPSQASILT EEVIRNWPER SKTLCSDFTA LESNDEKEDW LRTLFIELFD FINKNDENSP LKLSDVASFT NELVNHERQV SQASIVGKMF IAVSSTVPNI NDLTTISLCK LIPSLHEELF KFSWISSKLL NKEQTTLLRH LLKKSKYELK ...String:
MAEQTLLSKL NALSQKVIPP ASPSQASILT EEVIRNWPER SKTLCSDFTA LESNDEKEDW LRTLFIELFD FINKNDENSP LKLSDVASFT NELVNHERQV SQASIVGKMF IAVSSTVPNI NDLTTISLCK LIPSLHEELF KFSWISSKLL NKEQTTLLRH LLKKSKYELK KYNLLVENSV GYGQLVALLI LAYYDPDNFS KVSAYLKEIY HIMGKYSLDS IRTLDVILNV SSQFITEGYK FFIALLRKSD SWPSSHVANN SNYSSLNEGG NMIAANIISF NLSQYNEEVD KENYERYMDM CCILLKNGFV NFYSIWDNVK PEMEFLQEYI QNLETELEEE STKGVENPLA MAAALSTENE TDEDNALVVN DDVNMKDKIS EETNADIESK GKQKTQQDIL LFGKIKLLER LLIHGCVIPV IHVLKQYPKV LYVSESLSRY LGRVFEYLLN PLYTSMTSSG ESKDMATALM ITRIDNGILA HKPRLIHKYK THEPFESLEL NSSYVFYYSE WNSNLTPFAS VNDLFENSHI YLSIIGPYLG RIPTLLSKIS RIGVADIQKN HGSESLHVTI DKWIDYVRKF IFPATSLLQN NPIATSEVYE LMKFFPFEKR YFIYNEMMTK LSQDILPLKV SFNKAEREAK SILKALSIDT IAKESRRFAK LISTNPLASL VPAVKQIENY DKVSELVVYT TKYFNDFAYD VLQFVLLLRL TYNRPAVQFD GVNQAMWVQR LSIFIAGLAK NCPNMDISNI ITYILKTLHN GNIIAVSILK ELIITVGGIR DLNEVNMKQL LMLNSGSPLK QYARHLIYDF RDDNSVISSR LTSFFTDQSA ISEIILLLYT LNLKANTQNS HYKILSTRCD EMNTLLWSFI ELIKHCLKGK AFEENVLPFV ELNNRFHLST PWTFHIWRDY LDNQLNSNEN FSIDELIEGA EFSDVDLTKI SKDLFTTFWR LSLYDIHFDK SLYDERKNAL SGENTGHMSN RKKHLIQNQI KDILVTGISH QRAFKKTSEF ISEKSNVWNK DCGEDQIKIF LQNCVVPRVL FSPSDALFSS FFIFMAFRTE NLMSILNTCI TSNILKTLLF CCTSSEAGNL GLFFTDVLKK LEKMRLNGDF NDQASRKLYE WHSVITEQVI DLLSEKNYMS IRNGIEFMKH VTSVFPVVKA HIQLVYTTLE ENLINEERED IKLPSSALIG HLKARLKDAL ELDEFCTLTE EEAEQKRIRE MELEEIKNYE TACQNEQKQV ALRKQLELNK SQRLQNDPPK SVASGSAGLN SKDRYTYSRN EPVIPTKPSS SQWSYSKVTR HVDDINHYLA TNHLQKAISL VENDDETRNL RKLSKQNMPI FDFRNSTLEI FERYFRTLIQ NPQNPDFAEK IDSLKRYIKN ISREPYPDTT SSYSEAAAPE YTKRSSRYSG NAGGKDGYGS SNYRGPSNDR SAPKNIKPIS SYAHKRSELP TRPSKSKTYN DRSRALRPTG PDRGDGFDQR DNRLREEYKK NSSQRSQLRF PEKPFQEGKD SSKANPYQAS SYKRDSPSEN EEKPNKRFKK DETIRNKFQT QDYRNTRDSG AAHRANENQR YNGNRKSNTQ ALPQGPKGGN YVSRYQR

UniProtKB: THO complex subunit 2

-
Macromolecule #2: THO complex subunit HPR1

MacromoleculeName: THO complex subunit HPR1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MSNTEELIQN SIGFLQKTFK ALPVSFDSIR HEPLPSSMLH ASVLNFEWEP LEKNISAIHD RDSLIDIILK RFIIDSMTNA IEDEEENNLE KGLLNSCIGL DFVYNSRFNR SNPASWGNTF FELFSTIIDL LNSPSTFLKF WPYAESRIEW FKMNTSVEPV SLGESNLISY ...String:
MSNTEELIQN SIGFLQKTFK ALPVSFDSIR HEPLPSSMLH ASVLNFEWEP LEKNISAIHD RDSLIDIILK RFIIDSMTNA IEDEEENNLE KGLLNSCIGL DFVYNSRFNR SNPASWGNTF FELFSTIIDL LNSPSTFLKF WPYAESRIEW FKMNTSVEPV SLGESNLISY KQPLYEKLRH WNDILAKLEN NDILNTVKHY NMKYKLENFL SELLPINEES NFNRSASISA LQESDNEWNR SARERESNRS SDVIFAADYN FVFYHLIICP IEFAFSDLEY KNDVDRSLSP LLDAILEIEE NFYSKIKMNN RTRYSLEEAL NTEYYANYDV MTPKLPVYMK HSNAMKMDRN EFWANLQNIK ESDDYTLRPT IMDISLSNTT CLYKQLTQED DDYYRKQFIL QLCFTTNLIR NLISSDETRN FYKSCYLREN PLSDIDFENL DEVNKKRGLN LCSYICDNRV LKFYKIKDPD FYRVIRKLMS SDEKFTTAKI DGFKEFQNFR ISKEKIPPPA FDETFKKFTF IKMGNKLINN VWKIPTGLDK IEQEVKKPEG VYEAAQAKWE SKISSETSGG EAKDEIIRQW QTLRFLRSRY LFDFDKVNEK TGVDGLFEEP RKVEALDDSF KEKLLYKINQ EHRKKLQDAR EYKIGKERKK RALEEEASFP EREQKIKSQR INSASQTEGD ELKSEQTQPK GEISEENTKI KSSEVSSQDP DSGVAGEFAP QNTTAQLENP KTEDNNAATS NISNGSSTQD MKGSGSGSGS GSSAWSHPQF EKGGGSGGGS GGSAWSHPQF EK

UniProtKB: THO complex subunit HPR1

-
Macromolecule #3: THO complex subunit MFT1

MacromoleculeName: THO complex subunit MFT1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MPLSQKQIDQ VRTKVHYSEV DTPFNKYLDI LGKVTKLTGS IINGTLSNDD SKIEKLTEQN ISQLKESAHL RFLDLQSSID TKKVADENWE TCQQETLAKL ENLKDKLPDI KSIHSKLLLR IGKLQGLYDS VQVINREVEG LSEGRTSLVV TRAEWEKELG TDLVKFLIEK ...String:
MPLSQKQIDQ VRTKVHYSEV DTPFNKYLDI LGKVTKLTGS IINGTLSNDD SKIEKLTEQN ISQLKESAHL RFLDLQSSID TKKVADENWE TCQQETLAKL ENLKDKLPDI KSIHSKLLLR IGKLQGLYDS VQVINREVEG LSEGRTSLVV TRAEWEKELG TDLVKFLIEK NYLKLVDPGL KKDSSEERYR IYDDFSKGPK ELESINASMK SDIENVRQEV SSYKEKWLRD AEIFGKITSI FKEELLKRDG LLNEAEGDNI DEDYESDEDE ERKERFKRQR SMVEVNTIEN VDEKEESDHE YDDQEDEENE EEDDMEVDVE DIKEDNEVDG ESSQQEDNSR QGNNEETDKE TGVIEEPDAV NDAEEADSDH SSRKLGGTTS DFSASSSVEE VK

UniProtKB: THO complex subunit MFT1

-
Macromolecule #4: Protein TEX1

MacromoleculeName: Protein TEX1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MSTIGAVDIL NQKTITSEVA ASVTSKYLQS TFSKGNTSHI EDKRFIHVSS RSHSRFTSTP ITPNEILSLK FHVSGSSMAY SRMDGSLTVW FIKDASFDKS VEVYIPDCCG SDKLATDLSW NPTSLNQIAV VSNSSEISLL LINEKSLTAS KLRTLSLGSK TKVNTCLYDP ...String:
MSTIGAVDIL NQKTITSEVA ASVTSKYLQS TFSKGNTSHI EDKRFIHVSS RSHSRFTSTP ITPNEILSLK FHVSGSSMAY SRMDGSLTVW FIKDASFDKS VEVYIPDCCG SDKLATDLSW NPTSLNQIAV VSNSSEISLL LINEKSLTAS KLRTLSLGSK TKVNTCLYDP LGNWLLAATK SEKIYLFDVK KDHSSVCSLN ISDISQEDND VVYSLAWSNG GSHIFIGFKS GYLAILKAKH GILEVCTKIK AHTGPITEIK MDPWGRNFIT GSIDGNCYVW NMKSLCCELI INDLNSAVTT LDVCHLGKIL GICTEDEMVY FYDLNSGNLL HSKSLANYKT DPVLKFYPDK SWYIMSGKND TLSNHFVKNE KNLITYWKDM FDNTMIEKRR KNNGGGNNHN KRTSKNTDRI GKDRPSRFNS KK

UniProtKB: Protein TEX1

-
Macromolecule #5: THO complex subunit THP2

MacromoleculeName: THO complex subunit THP2 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae BY4741 (yeast)
SequenceString: MTKEEGRTYF ESLCEEEQSL QESQTHLLNI LDILSVLADP RSSDDLLTES LKKLPDLHRE LINSSIRLRY DKYQTREAQL LEDTKTGRDV AAGVQNPKSI SEYYSTFEHL NRDTLRYINL LKRLSVDLAK QVEVSDPSVT VYEMDKWVPS EKLQGILEQY CAPDTDIRGV ...String:
MTKEEGRTYF ESLCEEEQSL QESQTHLLNI LDILSVLADP RSSDDLLTES LKKLPDLHRE LINSSIRLRY DKYQTREAQL LEDTKTGRDV AAGVQNPKSI SEYYSTFEHL NRDTLRYINL LKRLSVDLAK QVEVSDPSVT VYEMDKWVPS EKLQGILEQY CAPDTDIRGV DAQIKNYLDQ IKMARAKFGL ENKYSLKERL STLTKELNHW RKEWDDIEML MFGDDAHSMK KMIQKIDSLK SEINAPSESY PVDKEGDIVL E

UniProtKB: THO complex subunit THP2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Component:
ConcentrationName
50.0 mMPotassium phosphate
0.01 %NP40
10.0 mMBiotin
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2258 / Average exposure time: 16.0 sec. / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 22000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio generated by cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 37404
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 3 / Avg.num./class: 30000 / Software - Name: cryoSPARC (ver. 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://pdbjlvh1.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