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- EMDB-52808: Cryo-EM structure of the kinetoplastid trans-spliceosome (Combine... -

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Basic information

Entry
Database: EMDB / ID: EMD-52808
TitleCryo-EM structure of the kinetoplastid trans-spliceosome (Combined C*/P complex) - PRP22/DHX8 focused map 1
Map dataB-factor sharpened map
Sample
  • Complex: Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in closed conformation bound to pre-mRNA
    • Protein or peptide: Splicing factor Cactin C-terminal domain-containing protein
    • Protein or peptide: RNA helicase
    • Protein or peptide: NF-kappa-B-activating protein C-terminal domain-containing protein
    • Protein or peptide: Probable RNA helicase
    • RNA: Pre-mRNA
KeywordsTrans-spliceosome / ATP-dependent RNA Helicase / Spliceosome / SPLICING
Function / homology
Function and homology information


spliceosomal complex disassembly / mRNA cis splicing, via spliceosome / catalytic step 2 spliceosome / spliceosomal complex / regulation of gene expression / RNA helicase activity / RNA helicase / hydrolase activity / chromatin binding / RNA binding ...spliceosomal complex disassembly / mRNA cis splicing, via spliceosome / catalytic step 2 spliceosome / spliceosomal complex / regulation of gene expression / RNA helicase activity / RNA helicase / hydrolase activity / chromatin binding / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
NF-kappa-B-activating protein, C-terminal / NF-kappa-B-activating protein / NF-kappa-B-activating protein C-terminal domain / Cactin, C-terminal / Cactus-binding C-terminus of cactin protein / Cactus-binding C-terminus of cactin protein / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold ...NF-kappa-B-activating protein, C-terminal / NF-kappa-B-activating protein / NF-kappa-B-activating protein C-terminal domain / Cactin, C-terminal / Cactus-binding C-terminus of cactin protein / Cactus-binding C-terminus of cactin protein / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Splicing factor Cactin C-terminal domain-containing protein / RNA helicase / NF-kappa-B-activating protein C-terminal domain-containing protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsNadenoen T / Vanden Broeck A
Funding support Belgium, European Union, 2 items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)MISU F.6005.25 Belgium
European Research Council (ERC)TranSplice 101162011European Union
CitationJournal: To Be Published
Title: Structural insights into Spliced Leader RNA trans-splicing in parasitic Trypanosomatids
Authors: Nadenoen T / Vanden Broeck A
History
DepositionFeb 12, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52808.png

Downloads & links

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Map

FileDownload / File: emd_52808.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å		1.07 Å/pix.
x 400 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0666
Minimum - Maximum-0.3532972 - 0.46926364
Average (Standard dev.)0.00017428424 (±0.004099976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52808_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_52808_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_52808_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in cl...

EntireName: Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in closed conformation bound to pre-mRNA
Components
  • Complex: Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in closed conformation bound to pre-mRNA
    • Protein or peptide: Splicing factor Cactin C-terminal domain-containing protein
    • Protein or peptide: RNA helicase
    • Protein or peptide: NF-kappa-B-activating protein C-terminal domain-containing protein
    • Protein or peptide: Probable RNA helicase
    • RNA: Pre-mRNA

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Supramolecule #1: Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in cl...

SupramoleculeName: Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in closed conformation bound to pre-mRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Leishmania tarentolae (eukaryote)

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Macromolecule #1: Splicing factor Cactin C-terminal domain-containing protein

MacromoleculeName: Splicing factor Cactin C-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 78.806461 KDa
SequenceString: MDWDRPSGKR RRTDEDEACE ALGGLLRQTA SRAMERVRLQ RQQRGWESQL TILSSSAAAA VVRSVKPMDV LVIRFCLYYL DCSTVAAAN HFVRLAQEVV TSSIERVLVP QLFSRDGSSL PALCEGLVTE HTAEEIQVTV KEVSEFVEAR GALGAWIADA T ATRGDRDD ...String:
MDWDRPSGKR RRTDEDEACE ALGGLLRQTA SRAMERVRLQ RQQRGWESQL TILSSSAAAA VVRSVKPMDV LVIRFCLYYL DCSTVAAAN HFVRLAQEVV TSSIERVLVP QLFSRDGSSL PALCEGLVTE HTAEEIQVTV KEVSEFVEAR GALGAWIADA T ATRGDRDD DDYDDYDDAD NYGGGYDDYS RSRDRDDGYS RLTNEEGEGD GEGDHGSPAS PHKDTNDFAL AITLYQACEF WA RVQAFLN SLSLHSAHLH VFAMPPRYER ELLLLLYTVT RGGGDHDEAS VEAVALAGGS ASRVGKGNNA GITPAEGASV SLS ANAVAA KVKKKEAIKQ ESMWDSDDEV AAPVAGENCT DVEGAENTDV VEGPRQPQQL YRASALLADV LALSRCPDVP TASS SPPAG TTSEVALISS PLSAAAPRIS AEATQRLQGL SPKFYKMVYA RLGVMVARDR LHRFDRVSAI TPPEFTVQQR NLQEQ LLQQ EQQQQYKADL MSAALGIPGQ PEAGLPAAYV PDDTYYEKLL HQQHDTIDED EEVYKGEVMD YYLSHPNRPG AATESS SSY SRARSHHRGS SARNGEAEPL MKPHRFCKVK MGFTWTQYNR THYDSRTNPP PRTEMWYEFT LFYPALAHTK RDMRHIF RI EDTPEGPNDQ YCLLVFSVGP PYADVAYRIR KKQWDTRRGG VRISFDQYGR YKLFFRFTNS NYRR

UniProtKB: Splicing factor Cactin C-terminal domain-containing protein

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Macromolecule #2: RNA helicase

MacromoleculeName: RNA helicase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 123.210883 KDa
SequenceString: MNAVGSTVGL VDSDDDAIAE QQNMSFLMKL QELYCKTVLY DQLEQMMGHP ATQEESDGYL DDVEGLVKLY YSEMEAAKKM VPKGEEPST AAQREVTEQH ILHSLSVAIN GGAEADEEPD VPISSIQKLY HVLHGCLTTD TVETGLAVGS LLLADDAKRS A EEAARLAY ...String:
MNAVGSTVGL VDSDDDAIAE QQNMSFLMKL QELYCKTVLY DQLEQMMGHP ATQEESDGYL DDVEGLVKLY YSEMEAAKKM VPKGEEPST AAQREVTEQH ILHSLSVAIN GGAEADEEPD VPISSIQKLY HVLHGCLTTD TVETGLAVGS LLLADDAKRS A EEAARLAY QQQQRHMHGG VDTASMNTST VERKNAMKVS PEEMFRLAQH VRSGLADEAE LLKLRSEDNE ENGDGAQDVE LN DEEPRFL RNMGFSSMLH RRINYRAPLP SQQLRDARTP QHRQAILDRL AQRQQGDTSK LNSMEAVAQM QEKINMDRRV IAR KAQRAQ QQSREYDFGA AISGREGKLV LDEGRYGRRG EALESEEYSV QPTLLHSELN ALPEEGGFRP QDLPTKLAPW MKHS FGNKP RFGLPETMQT IQEQRVSLPI YAKKEALLNF VDAHRVTVLV GETGSGKTTQ IPQYLAEHGY ADRGMIACTQ PRRVA AETL AMRVAEEYGC RLGEEVGYTV RFRDVTSSLT KIKYMTDGML LREALLDDSF QRYSVIILDE AHERSISTDL LFAIVR QAL RKNEVLKVMV TSATLETEKF CAYFGASEPF RIEGRTFPVE TYYLTDPTTD YVRTALQTVM MIHLQEPPGD VLVFFTG QE EIELGGEQLF RWMEMLRRQV STPLPDLMVL PLTATMPQEV QSKVFEPTPP GCRKVVLATN VAETSITITN LYYVVDSG F CKQNIFDAKH GIDQLKVMPV SQAQAKQRSG RAGRIGPGKC YRMYTEKQFT TDMVPETVPD IMRTSLFHVT LQLKAMGLD LLSLELMDCP PKGAIVSALE KLRYLEALDD DGLLTPLGSR MAQLSIDPSQ SKTLLTAVDL GCSEPVLTIV SMLAVQKRGV FYRPRDQQD ASDAARRQFM QPEGDQLTLM AVYDAWVENG MSEDWCKHNF LKHRMLVEAR DTRDQLKEML ARRNQHISHE N DTNLDEVR KSITAGYFFN AARRVDSHTR SYVTLSDRRE VYVHPSSVLI DDPPKYVLYD DLRMTKREYM TELLAIEPKW LV ELAPAFY AKPKEGRLTK EQAAERFTPI LKSWETGSSW RISRLKKQRR

UniProtKB: RNA helicase

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Macromolecule #3: NF-kappa-B-activating protein C-terminal domain-containing protein

MacromoleculeName: NF-kappa-B-activating protein C-terminal domain-containing protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 43.596113 KDa
SequenceString: MSNSVWALAV STTSPSDLPA GDEVEQIVCR SLEENAYSVQ GFWLWQSNFI QSRRRREQRR RRQRNDVASP TKEGSGESAP TRSEAEEAS LQRADEIRGY VSAVLHATGY PYPFASTADD AREGADDPAP STVTDAETAV TSDGLTPASL CSTITDSAAV S GEPPLKVN ...String:
MSNSVWALAV STTSPSDLPA GDEVEQIVCR SLEENAYSVQ GFWLWQSNFI QSRRRREQRR RRQRNDVASP TKEGSGESAP TRSEAEEAS LQRADEIRGY VSAVLHATGY PYPFASTADD AREGADDPAP STVTDAETAV TSDGLTPASL CSTITDSAAV S GEPPLKVN RGEGTGATAR IPARPASALA KFVAKARAQH CDLVEHAPVV VATVPARWAE LDEPGTQPGM GRKRIQFSDE PP LVKTPQL SSRGHIRRDN GDNDDDDSFT VQLPAHMGLQ SSSNKDKSDG HSMDAGAGGA GGAEAVAAKH PSQMTRAEFL SQF KRAPRR GEVGQTAEEI AAAEKLGYVM SGSRSVASRM YVDRIQRQLH EHEAAKLQQQ FRKVEDERMD DQLVLGLAQF INSK AKS

UniProtKB: NF-kappa-B-activating protein C-terminal domain-containing protein

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Macromolecule #4: Probable RNA helicase

MacromoleculeName: Probable RNA helicase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 128.35375 KDa
SequenceString: MDFSFPHFTR ASTDMVYTQP PLKSLLELVI EAKGRLGLVP QRDVVRHHPS SSPFSHFSDS DEEGEGADRN ANKAEVRQDA VLTTRTSWV PPSYLLDYFF SGEFLSVFLT LHGISASRPV SMLVPPLFTV RDAQLHPLVE AGLCSVLQDA LHSSSRQHRS G GGGGWREG ...String:
MDFSFPHFTR ASTDMVYTQP PLKSLLELVI EAKGRLGLVP QRDVVRHHPS SSPFSHFSDS DEEGEGADRN ANKAEVRQDA VLTTRTSWV PPSYLLDYFF SGEFLSVFLT LHGISASRPV SMLVPPLFTV RDAQLHPLVE AGLCSVLQDA LHSSSRQHRS G GGGGWREG VRGGRGGGGD GGGEGSYMES NAAGTSGGGP FMPYWKGPRQ HHLQGGVLGA GEGNDNEAAE QSASGAAHPR CV YAQHRVD DPAFILPPQR FLFRGLQQVA LPALLLGDHV LMGGPRGIGK RTAALLSVGA NVLAFTSNVD SGTAEETDAP PAL VEGEGG AAADGASAAV TGPVPISPAD AEALQQEAVE DTRDAATSRP EPVSPPAPRA LIVLSSYPEV LSAAHWLRSV FGAE AFTPY TFEKEGTALR PLFEVDTAEQ QPAALDGGSK AASSSDAFGH VGAMNTFPET TGTRRFIGPP VSLPFITDTI GAARA PELL LVDPTQTDSA PLHSETTAPA LAELAALVMN VPLPAQAADT AQATAGERAS GGDSKLKRRR HREDEVDSDV EADEEH VET RSSRTHRRHH RHRSERDEVE SEDDEIRRGR HREKRSPHSR SRHRHHSRHG DRRDRREEEG SRGERNASGH RSHRRHH RR SYESDDSDSD RDKGKWPIED EDTHSPRHSR HQRGCRDHRH HSSGGSVSRR HRSRSDERRS RHGSSRHRHH RSRHHRDH H DEDQRSVSSS STATSSPSSP GFQLARPPSL MPTNVEAELP MMPGNHVAPP AADELRALAL DSIVPPAVAN ETSAPSEKP QEAAEEDRRA ELSDVLHQRI PLLITTYHAL GMALGMVQGE ASALPPLEHV RVALLANLER VLMPPLKMSF AHSWWLSLVN ALDVECQFV VTADRMGNEV RGFLDSTIIP DAGERFVHFD QRDASIWAMM NVQVCAVPVD VPVSAAPPNG GSEGRPRISG S DIDAAKVA HVFSTIAEHM LRTGGHATHG KDDVAFQADC GGRGACVAVV CSTRREQSLV VTQLQRLFQD QANDTQAAKG VR VTEKVEL FRAAEAEVLV LTDAQLADPR VLRDLHQCTE VDLILHFSLS RTVMAQLKKE EIIDLLAQRG RAILGGSKQF CAR RWWRGT AMTSAAGGGA AFGVPSNAVD FEPVKVECQL LLTEHNVHGR VGSCVMEALR EVSDS

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Macromolecule #5: Pre-mRNA

MacromoleculeName: Pre-mRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Molecular weightTheoretical: 2.098203 KDa
SequenceString:
UUUUUUU

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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: 7.8
GridModel: Quantifoil R3.5/1 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 31410 / Average exposure time: 2.0 sec. / 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1214398
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 98912
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationSoftware: (Name: cryoSPARC (ver. 4.6.0), RELION)
FSC plot (resolution estimation)

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