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- EMDB-11859: yeast THO-Sub2 complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-11859
Titleyeast THO-Sub2 complex
Map data
Sample
  • Complex: yeast THO-Sub2 complex
    • Protein or peptide: THO complex subunit 2,Tho2
    • Protein or peptide: THO complex subunit HPR1
    • Protein or peptide: THO complex subunit THP2
    • Protein or peptide: THO complex subunit MFT1
    • Protein or peptide: Protein TEX1
    • Protein or peptide: ATP-dependent RNA helicase SUB2
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 / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair ...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 / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / stress granule assembly / transcription elongation by RNA polymerase II / spliceosomal complex / mRNA splicing, via spliceosome / mRNA processing / DNA recombination / RNA helicase activity / chromosome, telomeric region / nucleic acid binding / molecular adaptor activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
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 / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
THO complex subunit THP2 / THO complex subunit HPR1 / THO complex subunit MFT1 / THO complex subunit 2 / Protein TEX1 / ATP-dependent RNA helicase SUB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSchuller SK / Schuller JM / Prabu RJ / Baumgartner M / Bonneau F / basquin J / Conti E
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC Advanced Investigator Grant EXORICO Germany
German Research Foundation (DFG)GRK1721, SFB/TRR 237 Germany
CitationJournal: Elife / Year: 2020
Title: Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex.
Authors: Sandra K Schuller / Jan M Schuller / J Rajan Prabu / Marc Baumgärtner / Fabien Bonneau / Jérôme Basquin / Elena Conti /
Abstract: The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to ...The yeast THO complex is recruited to active genes and interacts with the RNA-dependent ATPase Sub2 to facilitate the formation of mature export-competent messenger ribonucleoprotein particles and to prevent the co-transcriptional formation of RNA:DNA-hybrid-containing structures. How THO-containing complexes function at the mechanistic level is unclear. Here, we elucidated a 3.4 Å resolution structure of THO-Sub2 by cryo-electron microscopy. THO subunits Tho2 and Hpr1 intertwine to form a platform that is bound by Mft1, Thp2, and Tex1. The resulting complex homodimerizes in an asymmetric fashion, with a Sub2 molecule attached to each protomer. The homodimerization interfaces serve as a fulcrum for a seesaw-like movement concomitant with conformational changes of the Sub2 ATPase. The overall structural architecture and topology suggest the molecular mechanisms of nucleic acid remodeling during mRNA biogenesis.
History
DepositionOct 20, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface level: 0.25
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  • Surface view with fitted model
  • Atomic models: PDB-7apx
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11859.png

Downloads & links

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Map

FileDownload / File: emd_11859.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.9197756 - 1.9290166
Average (Standard dev.)0.002495283 (±0.03999559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z414.000414.000414.000
α/β/γ90.00090.00090.000
start NX/NY/NZ79740
NX/NY/NZ93103213
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.9201.9290.002

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Supplemental data

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Sample components

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Entire : yeast THO-Sub2 complex

EntireName: yeast THO-Sub2 complex
Components
  • Complex: yeast THO-Sub2 complex
    • Protein or peptide: THO complex subunit 2,Tho2
    • Protein or peptide: THO complex subunit HPR1
    • Protein or peptide: THO complex subunit THP2
    • Protein or peptide: THO complex subunit MFT1
    • Protein or peptide: Protein TEX1
    • Protein or peptide: ATP-dependent RNA helicase SUB2

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Supramolecule #1: yeast THO-Sub2 complex

SupramoleculeName: yeast THO-Sub2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightExperimental: 431 kDa/nm

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Macromolecule #1: THO complex subunit 2,Tho2

MacromoleculeName: THO complex subunit 2,Tho2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 186.067094 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAASMAEQTL LSKLNALSQK VIPPASPSQA SILTEEVIRN WPERSKTLCS DFTALESNDE KEDWLRTLFI ELFDFINKND ENSPLKLSD VASFTNELVN HERQVSQASI VGKMFIAVSS TVPNINDLTT ISLCKLIPSL HEELFKFSWI SSKLLNKEQT T LLRHLLKK ...String:
GAASMAEQTL LSKLNALSQK VIPPASPSQA SILTEEVIRN WPERSKTLCS DFTALESNDE KEDWLRTLFI ELFDFINKND ENSPLKLSD VASFTNELVN HERQVSQASI VGKMFIAVSS TVPNINDLTT ISLCKLIPSL HEELFKFSWI SSKLLNKEQT T LLRHLLKK SKYELKKYNL LVENSVGYGQ LVALLILAYY DPDNFSKVSA YLKEIYHIMG KYSLDSIRTL DVILNVSSQF IT EGYKFFI ALLRKSDSWP SSHVANNSNY SSLNEGGNMI AANIISFNLS QYNEEVDKEN YERYMDMCCI LLKNGFVNFY SIW DNVKPE MEFLQEYIQN LETELEEEST KGVENPLAMA AALSTENETD EDNALVVNDD VNMKDKISEE TNADIESKGK QKTQ QDILL FGKIKLLERL LIHGCVIPVI HVLKQYPKVL YVSESLSRYL GRVFEYLLNP LYTSMTSSGE SKDMATALMI TRIDN GILA HKPRLIHKYK THEPFESLEL NSSYVFYYSE WNSNLTPFAS VNDLFENSHI YLSIIGPYLG RIPTLLSKIS RIGVAD IQK NHGSESLHVT IDKWIDYVRK FIFPATSLLQ NNPIATSEVY ELMKFFPFEK RYFIYNEMMT KLSQDILPLK VSFNKAE RE AKSILKALSI DTIAKESRRF AKLISTNPLA SLVPAVKQIE NYDKVSELVV YTTKYFNDFA YDVLQFVLLL RLTYNRPA V QFDGVNQAMW VQRLSIFIAG LAKNCPNMDI SNIITYILKT LHNGNIIAVS ILKELIITVG GIRDLNEVNM KQLLMLNSG SPLKQYARHL IYDFRDDNSV ISSRLTSFFT DQSAISEIIL LLYTLNLKAN TQNSHYKILS TRCDEMNTLL WSFIELIKHC LKGKAFEEN VLPFVELNNR FHLSTPWTFH IWRDYLDNQL NSNENFSIDE LIEGAEFSDV DLTKISKDLF TTFWRLSLYD I HFDKSLYD ERKNALSGEN TGHMSNRKKH LIQNQIKDIL VTGISHQRAF KKTSEFISEK SNVWNKDCGE DQIKIFLQNC VV PRVLFSP SDALFSSFFI FMAFRTENLM SILNTCITSN ILKTLLFCCT SSEAGNLGLF FTDVLKKLEK MRLNGDFNDQ ASR KLYEWH SVITEQVIDL LSEKNYMSIR NGIEFMKHVT SVFPVVKAHI QLVYTTLEEN LINEEREDIK LPSSALIGHL KARL KDALE LDEFCTLTEE EAEQKRIREM ELEEIKNYET ACQNEQKQVA LRKQLELNKS QRLQNDPPKS VASGSAGLNS KDRYT YSRN EPVIPTKPSS SQWSYSKVTR HVDDINHYLA TNHLQKAISL VENDDETRNL RKLSKQNMPI FDFRNSTLEI FERYFR TLI QNPQNPDFAE KIDSLKRYIK NISREPYPDT TSSYSEAAAP EYTKRSSRYS GNAGGKDGYG SSNYRGPSND RSAPKNI KP ISSYAHKRSE LPTRPSKSKT YNDRSRALRP TGPDRGDGFD QRDNRLREEY KKNSSQRSQL RFPEKPFQEG KDSSKANP Y QASSYKRDSP SENEEKPNKR FKKDETIRNK FQTQDYRNTR DSGAAHRANE NQRYNGNRKS NTQALPQGPK GGNYVSRYQ R(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #2: THO complex subunit HPR1

MacromoleculeName: THO complex subunit HPR1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 84.544047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSNTEELIQN SIGFLQKTFK ALPVSFDSIR HEPLPSSMLH ASVLNFEWEP LEKNISAIHD RDSLIDIILK RFIIDSMTNA IEDEEENNL EKGLLNSCIG LDFVYNSRFN RSNPASWGNT FFELFSTIID LLNSPSTFLK FWPYAESRIE WFKMNTSVEP V SLGESNLI ...String:
MSNTEELIQN SIGFLQKTFK ALPVSFDSIR HEPLPSSMLH ASVLNFEWEP LEKNISAIHD RDSLIDIILK RFIIDSMTNA IEDEEENNL EKGLLNSCIG LDFVYNSRFN RSNPASWGNT FFELFSTIID LLNSPSTFLK FWPYAESRIE WFKMNTSVEP V SLGESNLI SYKQPLYEKL RHWNDILAKL ENNDILNTVK HYNMKYKLEN FLSELLPINE ESNFNRSASI SALQESDNEW NR SARERES NRSSDVIFAA DYNFVFYHLI ICPIEFAFSD LEYKNDVDRS LSPLLDAILE IEENFYSKIK MNNRTRYSLE EAL NTEYYA NYDVMTPKLP VYMKHSNAMK MDRNEFWANL QNIKESDDYT LRPTIMDISL SNTTCLYKQL TQEDDDYYRK QFIL QLCFT TNLIRNLISS DETRNFYKSC YLRENPLSDI DFENLDEVNK KRGLNLCSYI CDNRVLKFYK IKDPDFYRVI RKLMS SDEK FTTAKIDGFK EFQNFRISKE KIPPPAFDET FKKFTFIKMG NKLINNVWKI PTGLDKIEQE VKKPEGVYEA AQAKWE SKI SSETSGGEAK DEIIRQWQTL RFLRSRYLFD FDKVNEKTGV DGLFEEPRKV EALDDSFKEK LLYKINQEHR KKLQDAR EY KIGKERKKRA LEEEASFPER EQKIKSQRIN SASQTEGDEL KSEQTQPKGE ISEENTKIKS SEVSSQDPDS GVAGEFAP

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Macromolecule #3: THO complex subunit THP2

MacromoleculeName: THO complex subunit THP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.340264 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTKEEGRTYF ESLCEEEQSL QESQTHLLNI LDILSVLADP RSSDDLLTES LKKLPDLHRE LINSSIRLRY DKYQTREAQL LEDTKTGRD VAAGVQNPKS ISEYYSTFEH LNRDTLRYIN LLKRLSVDLA KQVEVSDPSV TVYEMDKWVP SEKLQGILEQ Y CAPDTDIR ...String:
MTKEEGRTYF ESLCEEEQSL QESQTHLLNI LDILSVLADP RSSDDLLTES LKKLPDLHRE LINSSIRLRY DKYQTREAQL LEDTKTGRD VAAGVQNPKS ISEYYSTFEH LNRDTLRYIN LLKRLSVDLA KQVEVSDPSV TVYEMDKWVP SEKLQGILEQ Y CAPDTDIR GVDAQIKNYL DQIKMARAKF GLENKYSLKE RLSTLTKELN HWRKEWDDIE MLMFGDDAHS MKKMIQKIDS LK SEINAPS ESYPVDKEGD IVLE

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Macromolecule #4: THO complex subunit MFT1

MacromoleculeName: THO complex subunit MFT1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 45.055012 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPLSQKQIDQ VRTKVHYSEV DTPFNKYLDI LGKVTKLTGS IINGTLSNDD SKIEKLTEQN ISQLKESAHL RFLDLQSSID TKKVADENW ETCQQETLAK LENLKDKLPD IKSIHSKLLL RIGKLQGLYD SVQVINREVE GLSEGRTSLV VTRAEWEKEL G TDLVKFLI ...String:
MPLSQKQIDQ VRTKVHYSEV DTPFNKYLDI LGKVTKLTGS IINGTLSNDD SKIEKLTEQN ISQLKESAHL RFLDLQSSID TKKVADENW ETCQQETLAK LENLKDKLPD IKSIHSKLLL RIGKLQGLYD SVQVINREVE GLSEGRTSLV VTRAEWEKEL G TDLVKFLI EKNYLKLVDP GLKKDSSEER YRIYDDFSKG PKELESINAS MKSDIENVRQ EVSSYKEKWL RDAEIFGKIT SI FKEELLK RDGLLNEAEG DNIDEDYESD EDEERKERFK RQRSMVEVNT IENVDEKEES DHEYDDQEDE ENEEEDDMEV DVE DIKEDN EVDGESSQQE DNSRQGNNEE TDKETGVIEE PDAVNDAEEA DSDHSSRKLG GTTSDFSASS SVEEVK

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Macromolecule #5: Protein TEX1

MacromoleculeName: Protein TEX1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 42.315168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTIGAVDIL NQKTITSEVA ASVTSKYLQS TFSKGNTSHI EDKRFIHVSS RSHSRFTSTP ITPNEILSLK FHVSGSSMAY SRMDGSLTV WFIKDASFDK SVEVYIPDCC GSDKLATDLS WNPTSLNQIA VVSNSSEISL LLINEKSLTA SKLRTLSLGS K TKVNTCLY ...String:
MSTIGAVDIL NQKTITSEVA ASVTSKYLQS TFSKGNTSHI EDKRFIHVSS RSHSRFTSTP ITPNEILSLK FHVSGSSMAY SRMDGSLTV WFIKDASFDK SVEVYIPDCC GSDKLATDLS WNPTSLNQIA VVSNSSEISL LLINEKSLTA SKLRTLSLGS K TKVNTCLY DPLGNWLLAA TKSEKIYLFD VKKDHSSVCS LNISDISQED NDVVYSLAWS NGGSHIFIGF KSGYLAILKA KH GILEVCT KIKAHTGPIT EIKMDPWGRN FITGSIDGNC YVWNMKSLCC ELIINDLNSA VTTLDVCHLG KILGICTEDE MVY FYDLNS GNLLHSKSLA NYKTDPVLKF YPDKSWYIMS GKNDTLSNHF VKNEKNLITY WKDM

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Macromolecule #6: ATP-dependent RNA helicase SUB2

MacromoleculeName: ATP-dependent RNA helicase SUB2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 45.521004 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAASDKKGSY VGIHSTGFKD FLLKPELSRA IIDCGFEHPS EVQQHTIPQS IHGTDVLCQA KSGLGKTAVF VLSTLQQLDP VPGEVAVVV ICNARELAYQ IRNEYLRFSK YMPDVKTAVF YGGTPISKDA ELLKNKDTAP HIVVATPGRL KALVREKYID L SHVKNFVI ...String:
GAASDKKGSY VGIHSTGFKD FLLKPELSRA IIDCGFEHPS EVQQHTIPQS IHGTDVLCQA KSGLGKTAVF VLSTLQQLDP VPGEVAVVV ICNARELAYQ IRNEYLRFSK YMPDVKTAVF YGGTPISKDA ELLKNKDTAP HIVVATPGRL KALVREKYID L SHVKNFVI DECDKVLEEL DMRRDVQEIF RATPRDKQVM MFSATLSQEI RPICRRFLQN PLEIFVDDEA KLTLHGLQQY YI KLEEREK NRKLAQLLDD LEFNQVIIFV KSTTRANELT KLLNASNFPA ITVHGHMKQE ERIARYKAFK DFEKRICVST DVF GRGIDI ERINLAINYD LTNEADQYLH RVGRAGRFGT KGLAISFVSS KEDEEVLAKI QERFDVKIAE FPEEGIDPST YLNN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 298657

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7apx:
yeast THO-Sub2 complex

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