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- PDB-7dcq: cryo-EM structure of the DEAH-box helicase Prp2 -

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Entry
Database: PDB / ID: 7dcq
Titlecryo-EM structure of the DEAH-box helicase Prp2
ComponentsPRP2 isoform 1
KeywordsSPLICING / spliceosome / RNA splicing / Bact complex / DEAH-box ATPase/helicase / Prp2 / Spp2
Function / homology
Function and homology information


snoRNA splicing / generation of catalytic spliceosome for first transesterification step / ATP-dependent activity, acting on RNA / U2-type catalytic step 1 spliceosome / helicase activity / nucleic acid binding / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
: / 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 ...: / 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
PRP2 isoform 1 / Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBai, R. / Wan, R. / Yan, C. / Jia, Q. / Zhang, P. / Lei, J. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Science / Year: 2021
Title: Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2.
Authors: Rui Bai / Ruixue Wan / Chuangye Yan / Qi Jia / Jianlin Lei / Yigong Shi /
Abstract: Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the ...Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu from the N half and Arg from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing.
History
DepositionOct 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 6, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

Deposited unit
x: PRP2 isoform 1


Theoretical massNumber of molelcules
Total (without water)99,9471
Polymers99,9471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29080 Å2

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Components

#1: Protein PRP2 isoform 1 / Y55_G0047080.mRNA.1.CDS.1


Mass: 99947.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRP2, GI526_G0005089, PACBIOSEQ_LOCUS5743 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6A5Q5S8, UniProt: P20095*PLUS
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: DEAH-box ATPase/helicase Prp2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 101 kDa/nm / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174455 / Symmetry type: POINT

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