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- EMDB-31668: Dimer structure of yeast THO complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31668
TitleDimer structure of yeast THO complex
Map data
Sample
  • Complex: THO Complex
    • Protein or peptide: Hpr1p
  • Protein or peptide: Tho2p
  • Protein or peptide: Tex1p
  • Protein or peptide: Mft1p
  • Protein or peptide: Thp2p
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsChen C / Tan M / Wu Z / Wu J / Lei 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) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31668.png

Downloads & links

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Map

FileDownload / File: emd_31668.map.gz / Format: CCP4 / Size: 437.9 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 486 pix.
= 534.6 Å		1.1 Å/pix.
x 486 pix.
= 534.6 Å		1.1 Å/pix.
x 486 pix.
= 534.6 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: 0.006
Minimum - Maximum-0.028371487 - 0.060852066
Average (Standard dev.)8.314454e-06 (±0.0013160495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions486486486
Spacing486486486
CellA=B=C: 534.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : THO Complex

EntireName: THO Complex
Components
  • Complex: THO Complex
    • Protein or peptide: Hpr1p
  • Protein or peptide: Tho2p
  • Protein or peptide: Tex1p
  • Protein or peptide: Mft1p
  • Protein or peptide: Thp2p

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Supramolecule #1: THO Complex

SupramoleculeName: THO Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Hpr1p

MacromoleculeName: Hpr1p / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSNTEELIQN SIGFLQKTFK ALPVSFDSIR HEPLPSSMLH ASVLNFEWEP LEKNISAIHD RDSLIDIILK RFIIDSMTN AIEDEEENNL EKGLLNSCIG LDFVYNSRFN RSNPASWGNT FFELFSTIID LLNSPSTFLK F WPYAESRI EWFKMNTSVE PVSLGESNLI ...String:
MSNTEELIQN SIGFLQKTFK ALPVSFDSIR HEPLPSSMLH ASVLNFEWEP LEKNISAIHD RDSLIDIILK RFIIDSMTN AIEDEEENNL EKGLLNSCIG LDFVYNSRFN RSNPASWGNT FFELFSTIID LLNSPSTFLK F WPYAESRI EWFKMNTSVE PVSLGESNLI SYKQPLYEKL RHWNDILAKL ENNDILNTVK HYNMKYKLEN FL SELLPIN EESNFNRSAS ISALQESDNE WNRSARERES NRSSDVIFAA DYNFVFYHLI ICPIEFAFSD LEY KNDVDR SLSPLLDAIL EIEENFYSKI KMNNRTRYSL EEALNTEYYA NYDVMTPKLP VYMKHSNAMK MDRN EFWAN LQNIKESDDY TLRPTIMDIS LSNTTCLYKQ LTQEDDDYYR KQFILQLCFT TNLIRNLISS DETRN FYKS CYLRENPLSD IDFENLDEVN KKRGLNLCSY ICDNRVLKFY KIKDPDFYRV IRKLMSSDEK FTTAKI DGF KEFQNFRISK EKIPPPAFDE TFKKFTFIKM GNKLINNVWK IPTGLDKIEQ EVKKPEGVYE AAQAKWE SK ISSETSGGEA KDEIIRQWQT LRFLRSRYLF DFDKVNEKTG VDGLFEEPRK VEALDDSFKE KLLYKINQ E HRKKLQDARE YKIGKERKKR ALEEEASFPE REQKIKSQRI NSASQTEGDE LKSEQTQPKG EISEENTKI KSSEVSSQDP DSGVAGEFAP QNTTAQLENP KTEDNNAATS NISNGSSTQD MK

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Macromolecule #2: Tho2p

MacromoleculeName: Tho2p / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAEQTLLSKL NALSQKVIPP ASPSQASILT EEVIRNWPER SKTLCSDFTA LESNDEKEDW LRTLFIELFD FINKNDENS PLKLSDVASF TNELVNHERQ VSQASIVGKM FIAVSSTVPN INDLTTISLC KLIPSLHEEL F KFSWISSK LLNKEQTTLL RHLLKKSKYE ...String:
MAEQTLLSKL NALSQKVIPP ASPSQASILT EEVIRNWPER SKTLCSDFTA LESNDEKEDW LRTLFIELFD FINKNDENS PLKLSDVASF TNELVNHERQ VSQASIVGKM FIAVSSTVPN INDLTTISLC KLIPSLHEEL F KFSWISSK LLNKEQTTLL RHLLKKSKYE LKKYNLLVEN SVGYGQLVAL LILAYYDPDN FSKVSAYLKE IY HIMGKYS LDSIRTLDVI LNVSSQFITE GYKFFIALLR KSDSWPSSHV ANNSNYSSLN EGGNMIAANI ISF NLSQYN EEVDKENYER YMDMCCILLK NGFVNFYSIW DNVKPEMEFL QEYIQNLETE LEEESTKGVE NPLA MAAAL STENETDEDN ALVVNDDVNM KDKISEETNA DIESKGKQKT QQDILLFGKI KLLERLLIHG CVIPV IHVL KQYPKVLYVS ESLSRYLGRV FEYLLNPLYT SMTSSGESKD MATALMITRI DNGILAHKPR LIHKYK THE PFESLELNSS YVFYYSEWNS NLTPFASVND LFENSHIYLS IIGPYLGRIP TLLSKISRIG VADIQKN HG SESLHVTIDK WIDYVRKFIF PATSLLQNNP IATSEVYELM KFFPFEKRYF IYNEMMTKLS QDILPLKV S FNKAEREAKS ILKALSIDTI AKESRRFAKL ISTNPLASLV PAVKQIENYD KVSELVVYTT KYFNDFAYD VLQFVLLLRL TYNRPAVQFD GVNQAMWVQR LSIFIAGLAK NCPNMDISNI ITYILKTLHN GNIIAVSILK ELIITVGGI RDLNEVNMKQ LLMLNSGSPL KQYARHLIYD FRDDNSVISS RLTSFFTDQS AISEIILLLY T LNLKANTQ NSHYKILSTR CDEMNTLLWS FIELIKHCLK GKAFEENVLP FVELNNRFHL STPWTFHIWR DY LDNQLNS NENFSIDELI EGAEFSDVDL TKISKDLFTT FWRLSLYDIH FDKSLYDERK NALSGENTGH MSN RKKHLI QNQIKDILVT GISHQRAFKK TSEFISEKSN VWNKDCGEDQ IKIFLQNCVV PRVLFSPSDA LFSS FFIFM AFRTENLMSI LNTCITSNIL KTLLFCCTSS EAGNLGLFFT DVLKKLEKMR LNGDFNDQAS RKLYE WHSV ITEQVIDLLS EKNYMSIRNG IEFMKHVTSV FPVVKAHIQL VYTTLEENLI NEEREDIKLP SSALIG HLK ARLKDALELD EFCTLTEEEA EQKRIREMEL EEIKNYETAC QNEQKQVALR KQLELNKSQR LQNDPPK SV ASGSAGLNSK DRYTYSRNEP VIPTKPSSSQ WSYSKVTRHV DDINHYLATN HLQKAISLVE NDDETRNL R KLSKQNMPIF DFRNSTLEIF ERYFRTLIQN PQNPDFAEKI DSLKRYIKNI SREPYPDTTS SYSEAAAPE YTKRSSRYSG NAGGKDGYGS SNYRGPSNDR SAPKNIKPIS SYAHKRSELP TRPSKSKTYN DRSRALRPTG PDRGDGFDQ RDNRLREEYK KNSSQRSQLR FPEKPFQEGK DSSKANPYQA SSYKRDSPSE NEEKPNKRFK K DETIRNKF QTQDYRNTRD SGAAHRANEN QRYNGNRKSN TQALPQGPKG GNYVSRYQR

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Macromolecule #3: Tex1p

MacromoleculeName: Tex1p / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTIGAVDIL NQKTITSEVA ASVTSKYLQS TFSKGNTSHI EDKRFIHVSS RSHSRFTSTP ITPNEILSLK FHVSGSSMA YSRMDGSLTV WFIKDASFDK SVEVYIPDCC GSDKLATDLS WNPTSLNQIA VVSNSSEISL L LINEKSLT ASKLRTLSLG SKTKVNTCLY ...String:
MSTIGAVDIL NQKTITSEVA ASVTSKYLQS TFSKGNTSHI EDKRFIHVSS RSHSRFTSTP ITPNEILSLK FHVSGSSMA YSRMDGSLTV WFIKDASFDK SVEVYIPDCC GSDKLATDLS WNPTSLNQIA VVSNSSEISL L LINEKSLT ASKLRTLSLG SKTKVNTCLY DPLGNWLLAA TKSEKIYLFD VKKDHSSVCS LNISDISQED ND VVYSLAW SNGGSHIFIG FKSGYLAILK AKHGILEVCT KIKAHTGPIT EIKMDPWGRN FITGSIDGNC YVW NMKSLC CELIINDLNS AVTTLDVCHL GKILGICTED EMVYFYDLNS GNLLHSKSLA NYKTDPVLKF YPDK SWYIM SGKNDTLSNH FVKNEKNLIT YWKDMFDNTM IEKRRKNNGG GNNHNKRTSK NTDRIGKDRP SRFNS KK

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Macromolecule #4: Mft1p

MacromoleculeName: Mft1p / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPLSQKQIDQ VRTKVHYSEV DTPFNKYLDI LGKVTKLTGS IINGTLSNDD SKIEKLTEQN ISQLKESAHL RFLDLQSSI DTKKVADENW ETCQQETLAK LENLKDKLPD IKSIHSKLLL RIGKLQGLYD SVQVINREVE G LSEGRTSL VVTRAEWEKE LGTDLVKFLI ...String:
MPLSQKQIDQ VRTKVHYSEV DTPFNKYLDI LGKVTKLTGS IINGTLSNDD SKIEKLTEQN ISQLKESAHL RFLDLQSSI DTKKVADENW ETCQQETLAK LENLKDKLPD IKSIHSKLLL RIGKLQGLYD SVQVINREVE G LSEGRTSL VVTRAEWEKE LGTDLVKFLI EKNYLKLVDP GLKKDSSEER YRIYDDFSKG PKELESINAS MK SDIENVR QEVSSYKEKW LRDAEIFGKI TSIFKEELLK RDGLLNEAEG DNIDEDYESD EDEERKERFK RQR SMVEVN TIENVDEKEE SDHEYDDQED EENEEEDDME VDVEDIKEDN EVDGESSQQE DNSRQGNNEE TDKE TGVIE EPDAVNDAEE ADSDHSSRKL GGTTSDFSAS SSVEEVK

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Macromolecule #5: Thp2p

MacromoleculeName: Thp2p / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTKEEGRTYF ESLCEEEQSL QESQTHLLNI LDILSVLADP RSSDDLLTES LKKLPDLHRE LINSSIRLRY DKYQTREAQ LLEDTKTGRD VAAGVQNPKS ISEYYSTFEH LNRDTLRYIN LLKRLSVDLA KQVEVSDPSV T VYEMDKWV PSEKLQGILE QYCAPDTDIR ...String:
MTKEEGRTYF ESLCEEEQSL QESQTHLLNI LDILSVLADP RSSDDLLTES LKKLPDLHRE LINSSIRLRY DKYQTREAQ LLEDTKTGRD VAAGVQNPKS ISEYYSTFEH LNRDTLRYIN LLKRLSVDLA KQVEVSDPSV T VYEMDKWV PSEKLQGILE QYCAPDTDIR GVDAQIKNYL DQIKMARAKF GLENKYSLKE RLSTLTKELN HW RKEWDDI EMLMFGDDAH SMKKMIQKID SLKSEINAPS ESYPVDKEGD IVLE

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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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115764
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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