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- EMDB-18979: Cryo-EM structure of the human TREX complex -

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Basic information

Entry
Database: EMDB / ID: EMD-18979
TitleCryo-EM structure of the human TREX complex
Map dataStructure of the human TREX complex, map.
Sample
  • Complex: Human TREX complex
    • Protein or peptide: Spliceosome RNA helicase DDX39B
    • Protein or peptide: THO complex subunit 1
    • Protein or peptide: THO complex subunit 2
    • Protein or peptide: THO complex subunit 3
    • Protein or peptide: THO complex subunit 4
KeywordsmRNA export / GENE REGULATION
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / transcription export complex / C5-methylcytidine-containing RNA reader activity / U6 snRNP / regulation of mRNA export from nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / ATP-dependent protein binding / mRNA 3'-end processing ...THO complex / THO complex part of transcription export complex / transcription export complex / C5-methylcytidine-containing RNA reader activity / U6 snRNP / regulation of mRNA export from nucleus / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / ATP-dependent protein binding / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / ATP-dependent activity, acting on RNA / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / U4 snRNP / RNA Polymerase II Transcription Termination / stem cell division / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / blastocyst development / U6 snRNA binding / neuron development / mRNA export from nucleus / RHOBTB2 GTPase cycle / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / osteoblast differentiation / negative regulation of neuron projection development / regulation of gene expression / RNA helicase activity / nuclear speck / RNA helicase / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
THOC3 beta-propeller domain / Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / TREX component Tex1/THOC3 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 ...THOC3 beta-propeller domain / Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / TREX component Tex1/THOC3 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / 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 / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / 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 / G-protein beta WD-40 repeat / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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
Spliceosome RNA helicase DDX39B / THO complex subunit 4 / THO complex subunit 2 / THO complex subunit 1 / THO complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsHohmann U / Pacheco-Fiallos B / Plaschka C
Funding supportEuropean Union, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
H2020 Marie Curie Actions of the European Commission896416European Union
European Molecular Biology Organization (EMBO)ALTF_1175-2019European Union
CitationJournal: To Be Published
Title: A molecular switch orchestrates the export of human messenger RNA
Authors: Hohmann U / Pacheco-Fiallos B / Brennecke J / Plaschka C
History
DepositionNov 25, 2023-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18979.png

Downloads & links

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Map

FileDownload / File: emd_18979.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the human TREX complex, map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 352 pix.
= 436.48 Å		1.24 Å/pix.
x 352 pix.
= 436.48 Å		1.24 Å/pix.
x 352 pix.
= 436.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.602
Minimum - Maximum-1.697667 - 3.5141616
Average (Standard dev.)0.01982003 (±0.08676031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 436.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Structure of the human TREX complex, half map B.

Fileemd_18979_half_map_1.map
AnnotationStructure of the human TREX complex, half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of the human TREX complex, half map A.

Fileemd_18979_half_map_2.map
AnnotationStructure of the human TREX complex, half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human TREX complex

EntireName: Human TREX complex
Components
  • Complex: Human TREX complex
    • Protein or peptide: Spliceosome RNA helicase DDX39B
    • Protein or peptide: THO complex subunit 1
    • Protein or peptide: THO complex subunit 2
    • Protein or peptide: THO complex subunit 3
    • Protein or peptide: THO complex subunit 4

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Supramolecule #1: Human TREX complex

SupramoleculeName: Human TREX complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spliceosome RNA helicase DDX39B

MacromoleculeName: Spliceosome RNA helicase DDX39B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.05625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQA KSGMGKTAVF VLATLQQLEP VTGQVSVLVM CHTRELAFQI SKEYERFSKY MPNVKVAVFF GGLSIKKDEE V LKKNCPHI ...String:
MAENDVDNEL LDYEDDEVET AAGGDGAEAP AKKDVKGSYV SIHSSGFRDF LLKPELLRAI VDCGFEHPSE VQHECIPQAI LGMDVLCQA KSGMGKTAVF VLATLQQLEP VTGQVSVLVM CHTRELAFQI SKEYERFSKY MPNVKVAVFF GGLSIKKDEE V LKKNCPHI VVGTPGRILA LARNKSLNLK HIKHFILDEC DKMLEQLDMR RDVQEIFRMT PHEKQVMMFS ATLSKEIRPV CR KFMQDPM EIFVDDETKL TLHGLQQYYV KLKDNEKNRK LFDLLDVLEF NQVVIFVKSV QRCIALAQLL VEQNFPAIAI HRG MPQEER LSRYQQFKDF QRRILVATNL FGRGMDIERV NIAFNYDMPE DSDTYLHRVA RAGRFGTKGL AITFVSDEND AKIL NDVQD RFEVNISELP DEIDISSYIE QTR

UniProtKB: Spliceosome RNA helicase DDX39B

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Macromolecule #2: THO complex subunit 1

MacromoleculeName: THO complex subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 75.752156 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSPTPPLFSL PEARTRFTKS TREALNNKNI KPLLSTFSQV PGSENEKKCT LDQAFRGILE EEIINHSSCE NVLAIISLAI GGVTEGICT ASTPFVLLGD VLDCLPLDQC DTIFTFVEKN VATWKSNTFY SAGKNYLLRM CNDLLRRLSK SQNTVFCGRI Q LFLARLFP ...String:
MSPTPPLFSL PEARTRFTKS TREALNNKNI KPLLSTFSQV PGSENEKKCT LDQAFRGILE EEIINHSSCE NVLAIISLAI GGVTEGICT ASTPFVLLGD VLDCLPLDQC DTIFTFVEKN VATWKSNTFY SAGKNYLLRM CNDLLRRLSK SQNTVFCGRI Q LFLARLFP LSEKSGLNLQ SQFNLENVTV FNTNEQESTL GQKHTEDREE GMDVEEGEMG DEEAPTTCSI PIDYNLYRKF WS LQDYFRN PVQCYEKISW KTFLKYSEEV LAVFKSYKLD DTQASRKKME ELKTGGEHVY FAKFLTSEKL MDLQLSDSNF RRH ILLQYL ILFQYLKGQV KFKSSNYVLT DEQSLWIEDT TKSVYQLLSE NPPDGERFSK MVEHILNTEE NWNSWKNEGC PSFV KERTS DTKPTRIIRK RTAPEDFLGK GPTKKILMGN EELTRLWNLC PDNMEACKSE TREHMPTLEE FFEEAIEQAD PENMV ENEY KAVNNSNYGW RALRLLARRS PHFFQPTNQQ FKSLPEYLEN MVIKLAKELP PPSEEIKTGE DEDEEDNDAL LKENES PDV RRDKPVTGEQ IEVFANKLGE QWKILAPYLE MKDSEIRQIE CDSEDMKMRA KQLLVAWQDQ EGVHATPENL INALNKS GL SDLAESLTND NETNS

UniProtKB: THO complex subunit 1

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Macromolecule #3: THO complex subunit 2

MacromoleculeName: THO complex subunit 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 183.087734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAAAVVVPA EWIKNWEKSG RGEFLHLCRI LSENKSHDSS TYRDFQQALY ELSYHVIKGN LKHEQASNVL SDISEFREDM PSILADVFC ILDIETNCLE EKSKRDYFTQ LVLACLYLVS DTVLKERLDP ETLESLGLIK QSQQFNQKSV KIKTKLFYKQ Q KFNLLREE ...String:
MAAAAVVVPA EWIKNWEKSG RGEFLHLCRI LSENKSHDSS TYRDFQQALY ELSYHVIKGN LKHEQASNVL SDISEFREDM PSILADVFC ILDIETNCLE EKSKRDYFTQ LVLACLYLVS DTVLKERLDP ETLESLGLIK QSQQFNQKSV KIKTKLFYKQ Q KFNLLREE NEGYAKLIAE LGQDLSGSIT SDLILENIKS LIGCFNLDPN RVLDVILEVF ECRPEHDDFF ISLLESYMSM CE PQTLCHI LGFKFKFYQE PNGETPSSLY RVAAVLLQFN LIDLDDLYVH LLPADNCIMD EHKREIAEAK QIVRKLTMVV LSS EKMDER EKEKEKEEEK VEKPPDNQKL GLLEALLKIG DWQHAQNIMD QMPPYYAASH KLIALAICKL IHITIEPLYR RVGV PKGAK GSPVNALQNK RAPKQAESFE DLRRDVFNMF CYLGPHLSHD PILFAKVVRI GKSFMKEFQS DGSKQEDKEK TEVIL SCLL SITDQVLLPS LSLMDCNACM SEELWGMFKT FPYQHRYRLY GQWKNETYNS HPLLVKVKAQ TIDRAKYIMK RLTKEN VKP SGRQIGKLSH SNPTILFDYI LSQIQKYDNL ITPVVDSLKY LTSLNYDVLA YCIIEALANP EKERMKHDDT TISSWLQ SL ASFCGAVFRK YPIDLAGLLQ YVANQLKAGK SFDLLILKEV VQKMAGIEIT EEMTMEQLEA MTGGEQLKAE GGYFGQIR N TKKSSQRLKD ALLDHDLALP LCLLMAQQRN GVIFQEGGEK HLKLVGKLYD QCHDTLVQFG GFLASNLSTE DYIKRVPSI DVLCNEFHTP HDAAFFLSRP MYAHHISSKY DELKKSEKGS KQQHKVHKYI TSCEMVMAPV HEAVVSLHVS KVWDDISPQF YATFWSLTM YDLAVPHTSY EREVNKLKVQ MKAIDDNQEM PPNKKKKEKE RCTALQDKLL EEEKKQMEHV QRVLQRLKLE K DNWLLAKS TKNETITKFL QLCIFPRCIF SAIDAVYCAR FVELVHQQKT PNFSTLLCYD RVFSDIIYTV ASCTENEASR YG RFLCCML ETVTRWHSDR ATYEKECGNY PGFLTILRAT GFDGGNKADQ LDYENFRHVV HKWHYKLTKA SVHCLETGEY THI RNILIV LTKILPWYPK VLNLGQALER RVHKICQEEK EKRPDLYALA MGYSGQLKSR KSYMIPENEF HHKDPPPRNA VASV QNGPG GGPSSSSIGS ASKSDESSTE ETDKSRERSQ CGVKAVNKAS STTPKGNSSN GNSGSNSNKA VKENDKEKGK EKEKE KKEK TPATTPEARV LGKDGKEKPK EERPNKDEKA RETKERTPKS DKEKEKFKKE EKAKDEKFKT TVPNAESKST QERERE KEP SRERDIAKEM KSKENVKGGE KTPVSGSLKS PVPRSDIPEP EREQKRRKID THPSPSHSST VKDSLIELKE SSAKLYI NH TPPPLSKSKE REMDKKDLDK SRERSREREK KDEKDRKERK RDHSNNDREV PPDLTKRRKE ENGTMGVSKH KSESPCES P YPNEKDKEKN KSKSSGKEKG SDSFKSEKMD KISSGGKKES RHDKEKIEKK EKRDSSGGKE EKKHHKSSDK HR

UniProtKB: THO complex subunit 2

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Macromolecule #4: THO complex subunit 3

MacromoleculeName: THO complex subunit 3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.817617 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAVPAAAMGP SALGQSGPGS MAPWCSVSSG PSRYVLGMQE LFRGHSKTRE FLAHSAKVHS VAWSCDGRRL ASGSFDKTAS VFLLEKDRL VKENNYRGHG DSVDQLCWHP SNPDLFVTAS GDKTIRIWDV RTTKCIATVN TKGENINICW SPDGQTIAVG N KDDVVTFI ...String:
MAVPAAAMGP SALGQSGPGS MAPWCSVSSG PSRYVLGMQE LFRGHSKTRE FLAHSAKVHS VAWSCDGRRL ASGSFDKTAS VFLLEKDRL VKENNYRGHG DSVDQLCWHP SNPDLFVTAS GDKTIRIWDV RTTKCIATVN TKGENINICW SPDGQTIAVG N KDDVVTFI DAKTHRSKAE EQFKFEVNEI SWNNDNNMFF LTNGNGCINI LSYPELKPVQ SINAHPSNCI CIKFDPMGKY FA TGSADAL VSLWDVDELV CVRCFSRLDW PVRTLSFSHD GKMLASASED HFIDIAEVET GDKLWEVQCE SPTFTVAWHP KRP LLAFAC DDKDGKYDSS REAGTVKLFG LPNDS

UniProtKB: THO complex subunit 3

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Macromolecule #5: THO complex subunit 4

MacromoleculeName: THO complex subunit 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.233609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADKMDMSLD DIIKLNRSQR GGRGGGRGRG RAGSQGGRGG GAQAAARVNR GGGPIRNRPA IARGAAGGGG RNRPAPYSRP KQLPDKWQH DLFDSGFGGG AGVETGGKLL VSNLDFGVSD ADIQELFAEF GTLKKAAVHY DRSGRSLGTA DVHFERKADA L KAMKQYNG VPLDGRPMNI QLVTS

UniProtKB: THO complex subunit 4

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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: 7.9
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.75 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204147
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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