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- EMDB-31670: cryo-EM structure of yeast THO complex with Sub2 -

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Basic information

Entry
Database: EMDB / ID: EMD-31670
Titlecryo-EM structure of yeast THO complex with Sub2
Map data
Sample
  • Complex: THO-Sub2 Complex
    • Complex: yeast THO
      • Protein or peptide: THO complex subunit HPR1
      • Protein or peptide: THO complex subunit 2
      • Protein or peptide: Protein TEX1
      • Protein or peptide: THO complex subunit MFT1
      • Protein or peptide: THO complex subunit THP2
    • Complex: Sub2
      • Protein or peptide: ATP-dependent RNA helicase SUB2
KeywordsRNA transcription / TRANSCRIPTION
Function / homology
Function and homology information


nucleoplasmic THO complex / cellular response to azide / THO complex / THO complex part of transcription export complex / transcription export complex / positive regulation of transcription elongation by RNA polymerase I / Cdc73/Paf1 complex / mRNA 3'-end processing / positive regulation of transcription by RNA polymerase I / subtelomeric heterochromatin formation ...nucleoplasmic THO complex / cellular response to azide / THO complex / THO complex part of transcription export complex / transcription export complex / positive regulation of transcription elongation by RNA polymerase I / 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 / nucleic acid binding / chromosome, telomeric region / molecular adaptor activity / RNA helicase 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 domain / DEAD/DEAH box helicase / 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 / 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 / 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 S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen C / Tan M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Bull (Beijing) / Year: 2021
Title: Structural and functional insights into R-loop prevention and mRNA export by budding yeast THO-Sub2 complex.
Authors: Cong Chen / Ming Tan / Zhenfang Wu / Yuebin Zhang / Fanyang He / Yanjia Lu / Shaobai Li / Mi Cao / Guohui Li / Jian Wu / Hong Cheng / Ming Lei /
History
DepositionAug 10, 2021-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31670.png

Downloads & links

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Map

FileDownload / File: emd_31670.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 336 pix.
= 366.24 Å		1.09 Å/pix.
x 336 pix.
= 366.24 Å		1.09 Å/pix.
x 336 pix.
= 366.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.17825593 - 0.272752
Average (Standard dev.)-0.000017317596 (±0.006104517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 366.24002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_31670_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : THO-Sub2 Complex

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

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Supramolecule #1: THO-Sub2 Complex

SupramoleculeName: THO-Sub2 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Supramolecule #2: yeast THO

SupramoleculeName: yeast THO / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)

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Supramolecule #3: Sub2

SupramoleculeName: Sub2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6

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Macromolecule #1: THO complex subunit HPR1

MacromoleculeName: THO complex subunit HPR1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 87.938547 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 Q NTTAQLENPK TEDNNAATSN ISNGSSTQDM K

UniProtKB: THO complex subunit HPR1

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Macromolecule #2: THO complex subunit 2

MacromoleculeName: THO complex subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 184.163734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEQTLLSKL NALSQKVIPP ASPSQASILT EEVIRNWPER SKTLCSDFTA LESNDEKEDW LRTLFIELFD FINKNDENSP LKLSDVASF TNELVNHERQ VSQASIVGKM FIAVSSTVPN INDLTTISLC KLIPSLHEEL FKFSWISSKL LNKEQTTLLR H LLKKSKYE ...String:
MAEQTLLSKL NALSQKVIPP ASPSQASILT EEVIRNWPER SKTLCSDFTA LESNDEKEDW LRTLFIELFD FINKNDENSP LKLSDVASF TNELVNHERQ VSQASIVGKM FIAVSSTVPN INDLTTISLC KLIPSLHEEL FKFSWISSKL LNKEQTTLLR H LLKKSKYE LKKYNLLVEN SVGYGQLVAL LILAYYDPDN FSKVSAYLKE IYHIMGKYSL DSIRTLDVIL NVSSQFITEG YK FFIALLR KSDSWPSSHV ANNSNYSSLN EGGNMIAANI ISFNLSQYNE EVDKENYERY MDMCCILLKN GFVNFYSIWD NVK PEMEFL QEYIQNLETE LEEESTKGVE NPLAMAAALS TENETDEDNA LVVNDDVNMK DKISEETNAD IESKGKQKTQ QDIL LFGKI KLLERLLIHG CVIPVIHVLK QYPKVLYVSE SLSRYLGRVF EYLLNPLYTS MTSSGESKDM ATALMITRID NGILA HKPR LIHKYKTHEP FESLELNSSY VFYYSEWNSN LTPFASVNDL FENSHIYLSI IGPYLGRIPT LLSKISRIGV ADIQKN HGS ESLHVTIDKW IDYVRKFIFP ATSLLQNNPI ATSEVYELMK FFPFEKRYFI YNEMMTKLSQ DILPLKVSFN KAEREAK SI LKALSIDTIA KESRRFAKLI STNPLASLVP AVKQIENYDK VSELVVYTTK YFNDFAYDVL QFVLLLRLTY NRPAVQFD G VNQAMWVQRL SIFIAGLAKN CPNMDISNII TYILKTLHNG NIIAVSILKE LIITVGGIRD LNEVNMKQLL MLNSGSPLK QYARHLIYDF RDDNSVISSR LTSFFTDQSA ISEIILLLYT LNLKANTQNS HYKILSTRCD EMNTLLWSFI ELIKHCLKGK AFEENVLPF VELNNRFHLS TPWTFHIWRD YLDNQLNSNE NFSIDELIEG AEFSDVDLTK ISKDLFTTFW RLSLYDIHFD K SLYDERKN ALSGENTGHM SNRKKHLIQN QIKDILVTGI SHQRAFKKTS EFISEKSNVW NKDCGEDQIK IFLQNCVVPR VL FSPSDAL FSSFFIFMAF RTENLMSILN TCITSNILKT LLFCCTSSEA GNLGLFFTDV LKKLEKMRLN GDFNDQASRK LYE WHSVIT EQVIDLLSEK NYMSIRNGIE FMKHVTSVFP VVKAHIQLVY TTLEENLINE EREDIKLPSS ALIGHLKARL KDAL ELDEF CTLTEEEAEQ KRIREMELEE IKNYETACQN EQKQVALRKQ LELNKSQRLQ NDPPKSVASG SAGLNSKDRY TYSRN EPVI PTKPSSSQWS YSKVTRHVDD INHYLATNHL QKAISLVEND DETRNLRKLS KQNMPIFDFR NSTLEIFERY FRTLIQ NPQ NPDFAEKIDS LKRYIKNISR EPYPDTTSSY SEAAAPEYTK RSSRYSGNAG GKDGYGSSNY RGPSNDRSAP KNIKPIS SY AHKRSELPTR PSKSKTYNDR SRALRPTGPD RGDGFDQRDN RLREEYKKNS SQRSQLRFPE KPFQEGKDSS KANPYQAS S YKRDSPSENE EKPNKRFKKD ETIRNKFQTQ DYRNTRDSGA AHRANENQRY NGNRKSNTQA LPQGPKGGNY VSRYQR

UniProtKB: THO complex subunit 2

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Macromolecule #3: Protein TEX1

MacromoleculeName: Protein TEX1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 47.229652 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 WKDMFDNTMI EKRRKNNGGG NNHN KRTSK NTDRIGKDRP SRFNSKK

UniProtKB: Protein TEX1

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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 S288c (yeast) / Strain: 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

UniProtKB: THO complex subunit MFT1

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Macromolecule #5: THO complex subunit THP2

MacromoleculeName: THO complex subunit THP2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: 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

UniProtKB: THO complex subunit THP2

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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 S288c (yeast) / Strain: S288c
Molecular weightTheoretical: 50.375859 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSHEGEEDLL EYSDNEQEIQ IDASKAAEAG ETGAATSATE GDNNNNTAAG DKKGSYVGIH STGFKDFLLK PELSRAIIDC GFEHPSEVQ QHTIPQSIHG TDVLCQAKSG LGKTAVFVLS TLQQLDPVPG EVAVVVICNA RELAYQIRNE YLRFSKYMPD V KTAVFYGG ...String:
MSHEGEEDLL EYSDNEQEIQ IDASKAAEAG ETGAATSATE GDNNNNTAAG DKKGSYVGIH STGFKDFLLK PELSRAIIDC GFEHPSEVQ QHTIPQSIHG TDVLCQAKSG LGKTAVFVLS TLQQLDPVPG EVAVVVICNA RELAYQIRNE YLRFSKYMPD V KTAVFYGG TPISKDAELL KNKDTAPHIV VATPGRLKAL VREKYIDLSH VKNFVIDECD KVLEELDMRR DVQEIFRATP RD KQVMMFS ATLSQEIRPI CRRFLQNPLE IFVDDEAKLT LHGLQQYYIK LEEREKNRKL AQLLDDLEFN QVIIFVKSTT RAN ELTKLL NASNFPAITV HGHMKQEERI ARYKAFKDFE KRICVSTDVF GRGIDIERIN LAINYDLTNE ADQYLHRVGR AGRF GTKGL AISFVSSKED EEVLAKIQER FDVKIAEFPE EGIDPSTYLN N

UniProtKB: ATP-dependent RNA helicase SUB2

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 284361
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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