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- PDB-8q7x: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (St... -

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Entry
Database: PDB / ID: 8q7x
TitleStructure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 4)
Components
  • (Small nuclear ribonucleoprotein ...) x 6
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • CD2 antigen cytoplasmic tail-binding protein 2
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DDX23
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • U5 snRNA
KeywordsSPLICING / U5 snRNP / CD2BP2 / TSSC4 / spliceosome
Function / homology
Function and homology information


RNA localization / R-loop processing / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs ...RNA localization / R-loop processing / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / protein methylation / U12-type spliceosomal complex / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / sno(s)RNA-containing ribonucleoprotein complex / RNA splicing, via transesterification reactions / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / snRNP binding / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / commitment complex / telomerase RNA binding / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / RNA Polymerase II Transcription Termination / U2 snRNP / U1 snRNP / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / spliceosomal snRNP assembly / ribonucleoprotein complex binding / RNA processing / U1 snRNA binding / Cajal body / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / cellular response to xenobiotic stimulus / fibrillar center / mRNA processing / osteoblast differentiation / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / snRNP Assembly / protein-macromolecule adaptor activity / SARS-CoV-2 modulates host translation machinery / RNA helicase activity / nuclear speck / nuclear body / cilium / ciliary basal body / RNA helicase / intracellular membrane-bounded organelle / GTPase activity / mRNA binding / centrosome / chromatin / GTP binding / nucleolus / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / DDX23-like domain / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / : ...CD2 antigen cytoplasmic tail-binding protein 2/Lin1 / GYF domain / GYF-like domain superfamily / GYF domain / GYF domain profile. / Contains conserved Gly-Tyr-Phe residues / DDX23-like domain / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal / : / Small ribonucleoprotein associated, SmB/SmN / Small nuclear ribonucleoprotein D1 / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Winged Helix-turn-helix domain / Sec63 Brl domain / : / Tetratricopeptide repeat / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / Snu114, GTP-binding domain / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Pre-mRNA-splicing factor Syf1-like / Sec63 domain / Sec63 Brl domain / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / Tetratricopeptide repeat / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / : / Sm domain profile. / DEAD-box RNA helicase Q motif profile. / Elongation Factor G, domain II / Elongation Factor G, domain III / LSM domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / Translation elongation factor EFTu-like, domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Elongation factor Tu domain 2 / MPN domain / MPN domain profile. / Tetratricopeptide repeats / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / C2 domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Tetratricopeptide repeat / Helicase conserved C-terminal domain / Small GTP-binding protein domain / Tetratricopeptide-like helical domain superfamily / helicase superfamily c-terminal domain / Immunoglobulin E-set / WD domain, G-beta repeat / 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
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / CD2 antigen cytoplasmic tail-binding protein 2 / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E ...GUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / CD2 antigen cytoplasmic tail-binding protein 2 / Small nuclear ribonucleoprotein-associated proteins B and B' / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / 116 kDa U5 small nuclear ribonucleoprotein component / Pre-mRNA-processing-splicing factor 8 / U5 small nuclear ribonucleoprotein 40 kDa protein / Probable ATP-dependent RNA helicase DDX23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsRiabov Bassat, D. / Plaschka, C. / Vorlaender, M.K.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)ERC- 2020-STG 949081European Union
H2020 Marie Curie Actions of the European Commission101028744European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural basis of human U5 snRNP late biogenesis and recycling.
Authors: Daria Riabov Bassat / Supapat Visanpattanasin / Matthias K Vorländer / Laura Fin / Alexander W Phillips / Clemens Plaschka /
Abstract: Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP ...Pre-mRNA splicing by the spliceosome requires the biogenesis and recycling of its small nuclear ribonucleoprotein (snRNP) complexes, which are consumed in each round of splicing. The human U5 snRNP is the ~1 MDa 'heart' of the spliceosome and is recycled through an unknown mechanism involving major architectural rearrangements and the dedicated chaperones CD2BP2 and TSSC4. Late steps in U5 snRNP biogenesis similarly involve these chaperones. Here we report cryo-electron microscopy structures of four human U5 snRNP-CD2BP2-TSSC4 complexes, revealing how a series of molecular events primes the U5 snRNP to generate the ~2 MDa U4/U6.U5 tri-snRNP, the largest building block of the spliceosome.
History
DepositionAug 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
5: U5 snRNA
A: Pre-mRNA-processing-splicing factor 8
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: U5 small nuclear ribonucleoprotein 40 kDa protein
E: Probable ATP-dependent RNA helicase DDX23
F: Pre-mRNA-processing factor 6
G: CD2 antigen cytoplasmic tail-binding protein 2
a: Small nuclear ribonucleoprotein Sm D1
b: Small nuclear ribonucleoprotein-associated proteins B and B'
c: Small nuclear ribonucleoprotein Sm D2
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,040,74417
Polymers1,040,19615
Non-polymers5472
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

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RNA chain , 1 types, 1 molecules 5

#1: RNA chain U5 snRNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981

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Protein , 6 types, 6 molecules ACEFGb

#2: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 273974.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#4: Protein 116 kDa U5 small nuclear ribonucleoprotein component / Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP- ...Elongation factor Tu GTP-binding domain-containing protein 2 / SNU114 homolog / hSNU114 / U5 snRNP-specific protein / 116 kDa / U5-116 kDa


Mass: 109560.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#6: Protein Probable ATP-dependent RNA helicase DDX23 / 100 kDa U5 snRNP-specific protein / DEAD box protein 23 / PRP28 homolog / U5-100kD


Mass: 95785.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUQ8, RNA helicase
#7: Protein Pre-mRNA-processing factor 6 / Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP- ...Androgen receptor N-terminal domain-transactivating protein 1 / ANT-1 / PRP6 homolog / U5 snRNP-associated 102 kDa protein / U5-102 kDa protein


Mass: 107092.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O94906
#8: Protein CD2 antigen cytoplasmic tail-binding protein 2


Mass: 37841.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD2BP2 / Production host: Homo sapiens (human) / References: UniProt: O95400
#10: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules BD

#3: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 ...Activating signal cointegrator 1 complex subunit 3-like 1 / BRR2 homolog / U5 snRNP-specific 200 kDa protein / U5-200KD


Mass: 244823.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75643, RNA helicase
#5: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules acdefg

#9: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#11: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#12: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#13: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#14: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#15: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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Non-polymers , 2 types, 2 molecules

#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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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: Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 4, Map 4)
Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6879 / Symmetry type: POINT

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