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- PDB-9ibd: Kinetoplastid ATP-dependent RNA helicase PRP22/DHX8 in open confo... -

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Basic information

Entry
Database: PDB / ID: 9ibd
TitleKinetoplastid ATP-dependent RNA helicase PRP22/DHX8 in open conformation
Components
  • NF-kappa-B-activating protein C-terminal domain-containing protein
  • Probable RNA helicase
  • RNA helicase
  • Splicing factor Cactin C-terminal domain-containing protein
KeywordsSPLICING / Trans-spliceosome / ATP-dependent RNA Helicase / Spliceosome
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.69 Å
AuthorsNadenoen, T. / Vanden Broeck, A.
Funding support Belgium, European Union, 2items
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 basis for kinetoplastid SL trans-splicing
Authors: Nadenoen, T. / Vanden Broeck, A.
History
DepositionFeb 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
LF: Splicing factor Cactin C-terminal domain-containing protein
LV: RNA helicase
LZ: NF-kappa-B-activating protein C-terminal domain-containing protein
TN: Probable RNA helicase


Theoretical massNumber of molelcules
Total (without water)373,9674
Polymers373,9674
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 78806.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KRR3
#2: Protein RNA helicase / ATP-dependent RNA helicase DHX8/PRP22


Mass: 123210.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KVV3, RNA helicase
#3: Protein NF-kappa-B-activating protein C-terminal domain-containing protein


Mass: 43596.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10 / References: UniProt: A0A640KXH6
#4: Protein Probable RNA helicase


Mass: 128353.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / Cell line: P10
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Leishmania tarentolae ATP-dependant RNA helicase PRP22/DHX8 in open conformation
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania tarentolae (eukaryote)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 31410
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2SerialEMimage acquisition
4cryoSPARC4.6.0CTF correction
9PHENIX1.19.1model refinement
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13RELIONclassification
14cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1214398
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115573 / Symmetry type: POINT

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