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- PDB-8ro0: Structure of the C. elegans Intron Lariat Spliceosome primed for ... -

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Basic information

Entry
Database: PDB / ID: 8ro0
TitleStructure of the C. elegans Intron Lariat Spliceosome primed for disassembly (ILS')
Components
  • (Peptidyl-prolyl cis-trans ...) x 2
  • (Pre-mRNA-splicing factor ...) x 5
  • (Probable small nuclear ribonucleoprotein ...) x 4
  • (Small nuclear ribonucleoprotein Sm ...) x 2
  • (WD_REPEATS_REGION domain-containing ...) x 3
  • Cell division cycle 5-like protein
  • Coiled-coil domain-containing protein 12
  • GCF C-terminal domain-containing protein
  • Intron lariat RNA
  • Intron-binding protein aquarius
  • Pre-mRNA-processing factor 19
  • Probable U2 small nuclear ribonucleoprotein A'
  • Probable small nuclear ribonucleoprotein-associated protein B
  • Protein BUD31 homolog
  • Protein isy-1
  • RRM domain-containing protein
  • Septin and tuftelin-interacting protein 1 homolog
  • Spliceosome-associated protein CWC15 homolog
  • TPR_REGION domain-containing protein
  • Tr-type G domain-containing protein
  • U2 snRNA
  • U5 small nuclear ribonucleoprotein 200 kDa helicase
  • U5 snRNA
  • U6 snRNA
  • Uncharacterized protein T27F2.1
KeywordsSPLICING / mRNA / Intorn Lariat spliceosome / ILS / pre-mRNA
Function / homology
Function and homology information


feminization of hermaphroditic germ-line / molting cycle / regulation of primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / snRNP Assembly / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of Mature mRNA derived from an Intron-Containing Transcript / mRNA Splicing - Minor Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER ...feminization of hermaphroditic germ-line / molting cycle / regulation of primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / snRNP Assembly / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / Transport of Mature mRNA derived from an Intron-Containing Transcript / mRNA Splicing - Minor Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / germline cell cycle switching, mitotic to meiotic cell cycle / Downregulation of SMAD2/3:SMAD4 transcriptional activity / mRNA 3'-end processing / RNA Polymerase II Transcription Termination / vulval development / nematode larval development / egg-laying behavior / post-spliceosomal complex / U2-type post-mRNA release spliceosomal complex / spliceosomal complex disassembly / apoptotic DNA fragmentation / post-mRNA release spliceosomal complex / nuclear mRNA surveillance / generation of catalytic spliceosome for first transesterification step / nuclease activity / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / Prp19 complex / pICln-Sm protein complex / locomotion / snRNP binding / U2-type catalytic step 1 spliceosome / pre-mRNA binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / P granule / commitment complex / U2-type catalytic step 2 spliceosome / embryo development ending in birth or egg hatching / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / cyclosporin A binding / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / uterus development / germ cell development / protein K63-linked ubiquitination / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / peptidylprolyl isomerase / helicase activity / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / spliceosomal complex / RING-type E3 ubiquitin transferase / mRNA splicing, via spliceosome / mRNA processing / ubiquitin-protein transferase activity / metallopeptidase activity / ubiquitin protein ligase activity / protein folding / regulation of gene expression / nucleic acid binding / RNA helicase activity / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA helicase / cell division / intracellular membrane-bounded organelle / DNA repair / GTPase activity / mRNA binding / regulation of transcription by RNA polymerase II / GTP binding / apoptotic process / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
Intron Large complex component GCFC2-like / Tuftelin interacting protein, N-terminal domain / GCF, C-terminal / Septin and tuftelin interacting protein / : / GC-rich sequence DNA-binding factor-like protein / Tuftelin interacting protein N terminal / Nineteen complex-related protein 2 / mRNA splicing factor Cwf18-like / TFP11/STIP/Ntr1 ...Intron Large complex component GCFC2-like / Tuftelin interacting protein, N-terminal domain / GCF, C-terminal / Septin and tuftelin interacting protein / : / GC-rich sequence DNA-binding factor-like protein / Tuftelin interacting protein N terminal / Nineteen complex-related protein 2 / mRNA splicing factor Cwf18-like / TFP11/STIP/Ntr1 / cwf18 pre-mRNA splicing factor / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / Torus domain / Torus domain / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Pre-mRNA-splicing factor SPF27 / Breast carcinoma amplified sequence 2 (BCAS2) / Peptidyl-prolyl cis-trans isomerase E / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / CWF11 family / mRNA splicing factor SYF2 / SYF2 splicing factor / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / Helix hairpin bin domain superfamily / G-patch domain / Myb-like domain profile. / G-patch domain profile. / Pre-mRNA-processing factor 17 / G-patch domain / HAT (Half-A-TPR) repeat / glycine rich nucleic binding domain / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / Prp19/Pso4-like / U-box domain / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / G10 protein signature 1. / G10 protein signature 2. / : / STL11, N-terminal / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / DNA2/NAM7 helicase, helicase domain / Cwf15/Cwc15 cell cycle control protein / AAA domain / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / : / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / : / Myb-like DNA-binding domain / DNA2/NAM7-like helicase / Small nuclear ribonucleoprotein D1 / U-box domain profile. / Modified RING finger domain / Zinc finger, CCCH-type superfamily / U-box domain / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Sec63 Brl domain / zinc finger / : / Leucine-rich repeat / 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 / Myb-type HTH DNA-binding domain profile. / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm7/SmG / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / Small nuclear ribonucleoprotein Sm D1 / GCF C-terminal domain-containing protein / WD_REPEATS_REGION domain-containing protein / Cell division cycle 5-like protein / TPR_REGION domain-containing protein / WD_REPEATS_REGION domain-containing protein / Spliceosome-associated protein CWC15 homolog / Protein BUD31 homolog / Pre-mRNA-splicing factor 8 homolog / Probable small nuclear ribonucleoprotein F / Pre-mRNA-splicing factor SYF1 / Probable small nuclear ribonucleoprotein-associated protein B / Pre-mRNA-splicing factor syf-2 / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D3 / Septin and tuftelin-interacting protein 1 homolog / Peptidyl-prolyl cis-trans isomerase / Probable small nuclear ribonucleoprotein Sm D2 / WD_REPEATS_REGION domain-containing protein / Protein isy-1 / RRM domain-containing protein / Pre-mRNA-splicing factor RBM22 / Pre-mRNA-splicing factor SPF27 / Uncharacterized protein T27F2.1 / Tr-type G domain-containing protein / Coiled-coil domain-containing protein 12 / Probable U2 small nuclear ribonucleoprotein A' / Probable small nuclear ribonucleoprotein G / Intron-binding protein aquarius / U5 small nuclear ribonucleoprotein 200 kDa helicase / Peptidyl-prolyl cis-trans isomerase E / Probable small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsVorlaender, M.K. / Rothe, P. / Plaschka, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nature / Year: 2024
Title: Mechanism for the initiation of spliceosome disassembly.
Authors: Matthias K Vorländer / Patricia Rothe / Justus Kleifeld / Eric D Cormack / Lalitha Veleti / Daria Riabov-Bassat / Laura Fin / Alex W Phillips / Luisa Cochella / Clemens Plaschka /
Abstract: Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on ...Precursor-mRNA (pre-mRNA) splicing requires the assembly, remodelling and disassembly of the multi-megadalton ribonucleoprotein complex called the spliceosome. Recent studies have shed light on spliceosome assembly and remodelling for catalysis, but the mechanism of disassembly remains unclear. Here we report cryo-electron microscopy structures of nematode and human terminal intron lariat spliceosomes along with biochemical and genetic data. Our results uncover how four disassembly factors and the conserved RNA helicase DHX15 initiate spliceosome disassembly. The disassembly factors probe large inner and outer spliceosome surfaces to detect the release of ligated mRNA. Two of these factors, TFIP11 and C19L1, and three general spliceosome subunits, SYF1, SYF2 and SDE2, then dock and activate DHX15 on the catalytic U6 snRNA to initiate disassembly. U6 therefore controls both the start and end of pre-mRNA splicing. Taken together, our results explain the molecular basis of the initiation of canonical spliceosome disassembly and provide a framework to understand general spliceosomal RNA helicase control and the discard of aberrant spliceosomes.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: U2 snRNA
5: U5 snRNA
6: U6 snRNA
A: Pre-mRNA-splicing factor 8 homolog
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
C: Tr-type G domain-containing protein
D: Protein isy-1
E: WD_REPEATS_REGION domain-containing protein
I: Pre-mRNA-splicing factor SYF1
J: TPR_REGION domain-containing protein
K: Pre-mRNA-splicing factor SPF27
L: Cell division cycle 5-like protein
M: Pre-mRNA-splicing factor syf-2
N: Protein BUD31 homolog
O: Pre-mRNA-splicing factor RBM22
P: Spliceosome-associated protein CWC15 homolog
PX: GCF C-terminal domain-containing protein
Q: Intron-binding protein aquarius
R: Uncharacterized protein T27F2.1
S: Peptidyl-prolyl cis-trans isomerase
T: WD_REPEATS_REGION domain-containing protein
TF: Septin and tuftelin-interacting protein 1 homolog
W: WD_REPEATS_REGION domain-containing protein
Z: Coiled-coil domain-containing protein 12
a: Small nuclear ribonucleoprotein Sm D3
b: Probable small nuclear ribonucleoprotein-associated protein B
c: Small nuclear ribonucleoprotein Sm D1
d: Probable small nuclear ribonucleoprotein Sm D2
e: Probable small nuclear ribonucleoprotein E
f: Probable small nuclear ribonucleoprotein F
g: Probable small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein Sm D3
i: Probable small nuclear ribonucleoprotein-associated protein B
j: Small nuclear ribonucleoprotein Sm D1
k: Probable small nuclear ribonucleoprotein Sm D2
l: Probable small nuclear ribonucleoprotein E
m: Probable small nuclear ribonucleoprotein F
n: Probable small nuclear ribonucleoprotein G
o: Probable U2 small nuclear ribonucleoprotein A'
p: RRM domain-containing protein
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
y: Peptidyl-prolyl cis-trans isomerase E
In: Intron lariat RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,302,47262
Polymers2,300,06646
Non-polymers2,40616
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 , 3 types, 3 molecules 256

#1: RNA chain U2 snRNA


Mass: 56554.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Full sequence: AUCGCUUCUUCGGCUUAUUAGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCGUAUUAAC CUACGGUAUACACUCGAAUGAGUGUAAUAAAGGUUAUAUGAUUUUUGGAACCUAGGGAAG ACUCGGGGCUUGCUCCGACUUCCCAAGGGUCGUCCUGGCGUUGCACUGCUGCCGGGCUCGGCCCAGUCCCC
Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 6851
#2: RNA chain U5 snRNA


Mass: 38680.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 1200267
#3: RNA chain U6 snRNA


Mass: 32483.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: GenBank: 6866

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Pre-mRNA-splicing factor ... , 5 types, 5 molecules AIKMO

#4: Protein Pre-mRNA-splicing factor 8 homolog


Mass: 272396.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34369
#9: Protein Pre-mRNA-splicing factor SYF1


Mass: 99675.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91175
#11: Protein Pre-mRNA-splicing factor SPF27


Mass: 27679.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22417
#13: Protein Pre-mRNA-splicing factor syf-2


Mass: 27719.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q09385
#15: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22


Mass: 45902.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22412

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Protein , 16 types, 20 molecules BCDJLNPPXQRTFZbiopqrst

#5: Protein U5 small nuclear ribonucleoprotein 200 kDa helicase / BRR2 homolog


Mass: 244151.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U2G0, RNA helicase
#6: Protein Tr-type G domain-containing protein


Mass: 110612.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q23463
#7: Protein Protein isy-1


Mass: 31326.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q20716
#10: Protein TPR_REGION domain-containing protein


Mass: 88116.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O16376
#12: Protein Cell division cycle 5-like protein


Mass: 85843.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5EFC4
#14: Protein Protein BUD31 homolog / Protein G10 homolog


Mass: 17153.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34313
#16: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26154.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O45766
#17: Protein GCF C-terminal domain-containing protein


Mass: 94244.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5ECH1
#18: Protein Intron-binding protein aquarius


Mass: 170397.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U1Q7
#19: Protein Uncharacterized protein T27F2.1


Mass: 60303.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q22836
#22: Protein Septin and tuftelin-interacting protein 1 homolog / STIP-1


Mass: 94421.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q17784
#24: Protein Coiled-coil domain-containing protein 12


Mass: 19138.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q95XJ1
#26: Protein Probable small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / Sm-B / SmB


Mass: 16768.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P91918
#32: Protein Probable U2 small nuclear ribonucleoprotein A' / U2 snRNP A' / Masculinization of germline protein 2 / Spliceosome-associated protein mog-2


Mass: 28905.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9BLB6
#33: Protein RRM domain-containing protein


Mass: 24881.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q21323
#34: Protein
Pre-mRNA-processing factor 19 / PRP19/PSO4 homolog / RING-type E3 ubiquitin transferase PRP19


Mass: 53272.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata)
References: UniProt: Q10051, RING-type E3 ubiquitin transferase

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WD REPEATS REGION domain-containing ... , 3 types, 3 molecules ETW

#8: Protein WD_REPEATS_REGION domain-containing protein


Mass: 36865.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q19211
#21: Protein WD_REPEATS_REGION domain-containing protein


Mass: 54766.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: G5EEL2
#23: Protein WD_REPEATS_REGION domain-containing protein


Mass: 65385.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: O44729

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Peptidyl-prolyl cis-trans ... , 2 types, 2 molecules Sy

#20: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 18547.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q18445, peptidylprolyl isomerase
#35: Protein Peptidyl-prolyl cis-trans isomerase E / PPIase E


Mass: 36469.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9U2S6, peptidylprolyl isomerase

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Small nuclear ribonucleoprotein Sm ... , 2 types, 4 molecules ahcj

#25: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 14836.212 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q17348
#27: Protein Small nuclear ribonucleoprotein Sm D1 / snRNP core protein D1


Mass: 13724.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: E3LR34

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Probable small nuclear ribonucleoprotein ... , 4 types, 8 molecules dkelfmgn

#28: Protein Probable small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13291.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q18786
#29: Protein Probable small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 10625.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9XTU6
#30: Protein Probable small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


Mass: 9256.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: P34659
#31: Protein Probable small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8756.209 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata) / References: UniProt: Q9N4G9

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DNA chain , 1 types, 1 molecules In

#36: DNA chain Intron lariat RNA


Mass: 3680.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Caenorhabditis elegans (invertebrata)

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Non-polymers , 4 types, 16 molecules

#37: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#38: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#39: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#40: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: Intron lariat spliceosome / Type: COMPLEX / Entity ID: #1-#35 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Crosslinked with glutaraledhyde
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: 700 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7ISOLDEmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 879523 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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