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- PDB-8q7q: Structure of the recycling U5 snRNP bound to chaperones CD2BP2 an... -

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Entry
Database: PDB / ID: 8q7q
TitleStructure of the recycling U5 snRNP bound to chaperones CD2BP2 and TSSC4 (State 2)
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
  • Protein TSSC4
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • U5 snRNA
KeywordsSPLICING / U5 snRNP / CD2BP2 / TSSC4 / spliceosome
Function / homology
Function and homology information


RNA localization / 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 / protein methylation ...RNA localization / 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 / protein methylation / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / molecular sequestering activity / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / Cajal body / RNA processing / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / response to cocaine / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / fibrillar center / mRNA processing / osteoblast differentiation / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / snRNP Assembly / protein-macromolecule adaptor activity / SARS-CoV-2 modulates host translation machinery / cellular response to lipopolysaccharide / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / protein-containing complex binding / GTP binding / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Tumour suppressing sub-chromosomal transferable candidate 4 / Tumour suppressing sub-chromosomal transferable candidate 4 / 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 / PRP1 splicing factor, N-terminal / PRP1 splicing factor, N-terminal ...Tumour suppressing sub-chromosomal transferable candidate 4 / Tumour suppressing sub-chromosomal transferable candidate 4 / 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 / 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 / Tetratricopeptide repeat / Sec63 Brl domain / : / Pre-mRNA-splicing factor Syf1-like / 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 / 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 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / Tetratricopeptide repeat / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / Sm domain profile. / Elongation Factor G, domain II / Elongation Factor G, domain III / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / 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 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Tetratricopeptide repeats / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / C2 domain superfamily / Tetratricopeptide repeat / Helicase conserved C-terminal domain / Small GTP-binding protein domain / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Immunoglobulin E-set / 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 / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / G-protein beta WD-40 repeat
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 / Small nuclear ribonucleoprotein F ...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 / U5 small nuclear ribonucleoprotein TSSC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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 16, 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

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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
F: Pre-mRNA-processing factor 6
G: CD2 antigen cytoplasmic tail-binding protein 2
H: Protein TSSC4
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)979,32517
Polymers978,77815
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)

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Protein , 6 types, 6 molecules ACFGHb

#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) / Cell line: k562 / 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 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
#7: Protein CD2 antigen cytoplasmic tail-binding protein 2


Mass: 37841.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the N-terminal GP comes from a cleaved 3C tag / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): K562 cells / Production host: Homo sapiens (human) / References: UniProt: O95400
#8: Protein Protein TSSC4 / Tumor-suppressing STF cDNA 4 protein / Tumor-suppressing subchromosomal transferable fragment ...Tumor-suppressing STF cDNA 4 protein / Tumor-suppressing subchromosomal transferable fragment candidate gene 4 protein


Mass: 34366.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5U2
#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 chaperones CD2BP2 and TSSC4 (State , Map 2)
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19393 / Symmetry type: POINT

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