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- PDB-6qx9: Structure of a human fully-assembled precatalytic spliceosome (pr... -

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Basic information

Entry
Database: PDB / ID: 6qx9
TitleStructure of a human fully-assembled precatalytic spliceosome (pre-B complex).
Components
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 5
  • (U1 small nuclear ribonucleoprotein ...) x 3
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U4/U6 small nuclear ribonucleoprotein ...) x 3
  • (U4/U6.U5 tri-snRNP-associated protein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • AdML pre-mRNA
  • NHP2-like protein 1
  • PHD finger-like domain-containing protein 5A
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Probable ATP-dependent RNA helicase DDX23
  • RNA-binding protein 42
  • Serine/threonine-protein kinase PRP4 homolog
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Thioredoxin-like protein 4A
  • U1 snRNA
  • U2 snRNA
  • U4 snRNA
  • U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
  • U5 snRNA
  • U6 snRNA
KeywordsSPLICING / RNP complex / RNA / protein / spliceosome
Function / homology
Function and homology information


mRNA Splicing - Minor Pathway / negative regulation of protein refolding / mRNA Splicing - Major Pathway / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA ...mRNA Splicing - Minor Pathway / negative regulation of protein refolding / mRNA Splicing - Major Pathway / Lsm2-8 complex / U6 snRNA 3'-end binding / spliceosomal snRNP complex / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / R-loop processing / regulation of ATP-dependent activity / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / positive regulation of hippo signaling / regulation of mitotic cell cycle spindle assembly checkpoint / U6 snRNP / box C/D sno(s)RNA binding / U11/U12 snRNP / PH domain binding / dense fibrillar component / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / B-WICH complex / 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 / box C/D methylation guide snoRNP complex / protein methylation / splicing factor binding / U4/U6 snRNP / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / pICln-Sm protein complex / P-body assembly / sno(s)RNA-containing ribonucleoprotein complex / snRNP binding / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / small nuclear ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / telomerase RNA binding / spliceosomal tri-snRNP complex / telomerase holoenzyme complex / P granule / U2-type spliceosomal complex / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / negative regulation of chaperone-mediated autophagy / U3 snoRNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / U4 snRNP / positive regulation of mRNA splicing, via spliceosome / U2 snRNP / SAGA complex / rRNA modification in the nucleus and cytosol / RNA Polymerase II Transcription Termination / positive regulation of transcription by RNA polymerase III / U1 snRNP / pre-mRNA 5'-splice site binding / U2-type prespliceosome / tRNA processing / nuclear androgen receptor binding / precatalytic spliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / mRNA catabolic process / regulation of RNA splicing / mRNA 5'-splice site recognition / negative regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process / mRNA 3'-splice site recognition / MLL1 complex / spliceosomal tri-snRNP complex assembly / protein deubiquitination / single fertilization / U5 snRNA binding / U5 snRNP / Major pathway of rRNA processing in the nucleolus and cytosol / U2 snRNA binding / U6 snRNA binding / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of DNA repair / Cajal body / RNA processing
Similarity search - Function
snRNP70, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoprotein 27kDa protein / RBM42, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoproteins / Serine/threonine-protein PRP4, catalytic domain / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / : ...snRNP70, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoprotein 27kDa protein / RBM42, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoproteins / Serine/threonine-protein PRP4, catalytic domain / U1 small nuclear ribonucleoprotein C / U1 small nuclear ribonucleoprotein of 70kDa N-terminal / U1 small nuclear ribonucleoprotein of 70kDa MW N terminal / : / : / USP39 / U1-C, C2H2-type zinc finger / U1 zinc finger / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / Sm-like protein Lsm8 / PWI domain superfamily / PWI domain / PWI domain profile. / SF3B4, RNA recognition motif 2 / U6 snRNA-associated Sm-like protein Lsm1/8 / Pre-mRNA processing factor 4 (PRP4)-like / U6 snRNA-associated Sm-like protein LSm2 / Splicing factor SF3a60 binding domain / Sm-like protein Lsm4 / Splicing factor SF3a60 binding domain / Splicing Factor Motif, present in Prp18 and Pr04 / Sm-like protein Lsm7 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / Cactus-binding C-terminus of cactin protein / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / pre-mRNA processing factor 3 domain / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Splicing factor 3A subunit 1, ubiquitin domain / Prp31 C terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / : / Replication stress response SDE2 C-terminal / PWI domain / PWI, domain in splicing factors / Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / PRP1 splicing factor, N-terminal / SF3A2 domain / : / PRP1 splicing factor, N-terminal / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / SF3B4, RNA recognition motif 1 / : / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / Splicing factor 3B, subunit 5 / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / : / Splicing factor 3B subunit 1 / : / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / : / Zinc-finger of C2H2 type / PHF5-like / PHF5-like protein / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / Splicing factor 3B subunit 5/RDS3 complex subunit 10 / Splicing factor 3B subunit 10 (SF3b10) / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Small ribonucleoprotein associated, SmB/SmN / : / : / Small nuclear ribonucleoprotein D1 / H/ACA ribonucleoprotein complex, subunit Nhp2-like / NOSIC
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 / U4/U6 small nuclear ribonucleoprotein Prp3 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / RNA (> 100) / U4/U6 small nuclear ribonucleoprotein Prp4 / U4/U6.U5 tri-snRNP-associated protein 1 / U4/U6 small nuclear ribonucleoprotein Prp3 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / U6 snRNA-associated Sm-like protein LSm8 / U2 small nuclear ribonucleoprotein B'' / U1 small nuclear ribonucleoprotein 70 kDa / U1 small nuclear ribonucleoprotein A / U1 small nuclear ribonucleoprotein C / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / NHP2-like protein 1 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein G / U6 snRNA-associated Sm-like protein LSm3 / U6 snRNA-associated Sm-like protein LSm6 / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein Sm D3 / Thioredoxin-like protein 4A / Splicing factor 3A subunit 3 / Splicing factor 3B subunit 2 / Serine/threonine-protein kinase PRP4 homolog / 116 kDa U5 small nuclear ribonucleoprotein component / Splicing factor 3B subunit 3 / Splicing factor 3B subunit 4 / Splicing factor 3A subunit 2 / Splicing factor 3A subunit 1 / Ubiquitin carboxyl-terminal hydrolase 39 / Pre-mRNA-processing-splicing factor 8 / PHD finger-like domain-containing protein 5A / U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein / U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 6 / U5 small nuclear ribonucleoprotein 40 kDa protein / RNA-binding protein 42 / Probable ATP-dependent RNA helicase DDX23 / Splicing factor 3B subunit 5 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human adenovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsCharenton, C. / Wilkinson, M.E. / Nagai, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research CouncilAdG-693087-SPLICE3D United Kingdom
Medical Research Council (United Kingdom)MC_U105184330 United Kingdom
CitationJournal: Science / Year: 2019
Title: Mechanism of 5' splice site transfer for human spliceosome activation.
Authors: Clément Charenton / Max E Wilkinson / Kiyoshi Nagai /
Abstract: The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 ...The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Oct 7, 2020Group: Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity_poly / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_poly.pdbx_seq_one_letter_code ..._chem_comp.pdbx_synonyms / _entity_poly.pdbx_seq_one_letter_code / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Assembly

Deposited unit
1: U1 snRNA
6: U6 snRNA
5O: U5 small nuclear ribonucleoprotein 40 kDa protein
B4: Splicing factor 3B subunit 4
13: Small nuclear ribonucleoprotein Sm D3
4B: U4/U6 small nuclear ribonucleoprotein Prp4
5e: Small nuclear ribonucleoprotein E
I: AdML pre-mRNA
1K: U1 small nuclear ribonucleoprotein 70 kDa
4C: U4/U6 small nuclear ribonucleoprotein Prp31
41: Small nuclear ribonucleoprotein Sm D1
R: RNA-binding protein 42
1f: Small nuclear ribonucleoprotein F
4e: Small nuclear ribonucleoprotein E
66: U6 snRNA-associated Sm-like protein LSm6
X: U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein
22: Small nuclear ribonucleoprotein Sm D2
5: U5 snRNA
67: U6 snRNA-associated Sm-like protein LSm7
62: U6 snRNA-associated Sm-like protein LSm2
2B: U2 small nuclear ribonucleoprotein B''
53: Small nuclear ribonucleoprotein Sm D3
A2: Splicing factor 3A subunit 2
B2: Splicing factor 3B subunit 2
2f: Small nuclear ribonucleoprotein F
5C: 116 kDa U5 small nuclear ribonucleoprotein component
5X: Probable ATP-dependent RNA helicase DDX23
11: Small nuclear ribonucleoprotein Sm D1
42: Small nuclear ribonucleoprotein Sm D2
1b: Small nuclear ribonucleoprotein-associated proteins B and B'
B5: Splicing factor 3B subunit 5
1A: U1 small nuclear ribonucleoprotein A
S: U4/U6.U5 tri-snRNP-associated protein 1
5f: Small nuclear ribonucleoprotein F
5J: Pre-mRNA-processing factor 6
51: Small nuclear ribonucleoprotein Sm D1
4D: NHP2-like protein 1
63: U6 snRNA-associated Sm-like protein LSm3
2b: Small nuclear ribonucleoprotein-associated proteins B and B'
2: U2 snRNA
4f: Small nuclear ribonucleoprotein F
B3: Splicing factor 3B subunit 3
1g: Small nuclear ribonucleoprotein G
23: Small nuclear ribonucleoprotein Sm D3
5b: Small nuclear ribonucleoprotein-associated proteins B and B'
68: U6 snRNA-associated Sm-like protein LSm8
43: Small nuclear ribonucleoprotein Sm D3
1e: Small nuclear ribonucleoprotein E
5A: Pre-mRNA-processing-splicing factor 8
A3: Splicing factor 3A subunit 3
U: U4/U6.U5 tri-snRNP-associated protein 2
2g: Small nuclear ribonucleoprotein G
5D: Thioredoxin-like protein 4A
52: Small nuclear ribonucleoprotein Sm D2
12: Small nuclear ribonucleoprotein Sm D2
64: U6 snRNA-associated Sm-like protein LSm4
2e: Small nuclear ribonucleoprotein E
BP: PHD finger-like domain-containing protein 5A
1C: U1 small nuclear ribonucleoprotein C
5g: Small nuclear ribonucleoprotein G
K: Serine/threonine-protein kinase PRP4 homolog
4b: Small nuclear ribonucleoprotein-associated proteins B and B'
4A: U4/U6 small nuclear ribonucleoprotein Prp3
21: Small nuclear ribonucleoprotein Sm D1
4g: Small nuclear ribonucleoprotein G
4: U4 snRNA
2A: U2 small nuclear ribonucleoprotein A'
A1: Splicing factor 3A subunit 1,Splicing factor 3A subunit 1,Splicing factor 3A subunit 1
65: U6 snRNA-associated Sm-like protein LSm5
5B: U5 small nuclear ribonucleoprotein 200 kDa helicase
B1: Splicing factor 3B subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,871,62280
Polymers2,870,02271
Non-polymers1,6009
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 6 types, 6 molecules 16I524

#1: RNA chain U1 snRNA


Mass: 52697.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#8: RNA chain AdML pre-mRNA


Mass: 15279.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human adenovirus 2
#17: RNA chain U5 snRNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#32: RNA chain U2 snRNA


Mass: 60170.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#45: RNA chain U4 snRNA


Mass: 46997.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules 5O5B

#3: 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
#49: 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

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Splicing factor 3B subunit ... , 5 types, 5 molecules B4B2B5B3B1

#4: Protein Splicing factor 3B subunit 4 / Pre-mRNA-splicing factor SF3b 49 kDa subunit / Spliceosome-associated protein 49 / SAP 49


Mass: 44436.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15427
#22: Protein Splicing factor 3B subunit 2 / Pre-mRNA-splicing factor SF3b 145 kDa subunit / SF3b145 / Spliceosome-associated protein 145 / SAP 145


Mass: 100377.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13435
#26: Protein Splicing factor 3B subunit 5 / SF3b5 / Pre-mRNA-splicing factor SF3b 10 kDa subunit


Mass: 10149.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BWJ5
#33: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15393
#50: Protein Splicing factor 3B subunit 1 / Pre-mRNA-splicing factor SF3b 155 kDa subunit / SF3b155 / Spliceosome-associated protein 155 / SAP 155


Mass: 146024.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75533

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Small nuclear ribonucleoprotein ... , 6 types, 24 molecules 135323435e4e1e2e411151211f2f5f4f224252121g2g5g4g

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


Mass: 13940.308 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#7: Protein
Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10817.601 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#11: Protein
Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#13: Protein
Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#16: Protein
Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#34: Protein
Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8508.084 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308

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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules 4B4C4A

#6: Protein U4/U6 small nuclear ribonucleoprotein Prp4 / PRP4 homolog / hPrp4 / U4/U6 snRNP 60 kDa protein / WD splicing factor Prp4


Mass: 58536.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43172
#10: Protein U4/U6 small nuclear ribonucleoprotein Prp31 / Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP ...Pre-mRNA-processing factor 31 / Serologically defined breast cancer antigen NY-BR-99 / U4/U6 snRNP 61 kDa protein / hPrp31


Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3
#44: Protein U4/U6 small nuclear ribonucleoprotein Prp3 / Pre-mRNA-splicing factor 3 / hPrp3 / U4/U6 snRNP 90 kDa protein


Mass: 77669.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43395

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U1 small nuclear ribonucleoprotein ... , 3 types, 3 molecules 1K1A1C

#9: Protein U1 small nuclear ribonucleoprotein 70 kDa / snRNP70


Mass: 51683.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08621
#27: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 31319.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09012
#42: Protein U1 small nuclear ribonucleoprotein C / U1C


Mass: 17415.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09234

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Protein , 11 types, 14 molecules RX5C5X1b2b5b4b5J4D5A5DBPK

#12: Protein RNA-binding protein 42 / RNA-binding motif protein 42


Mass: 50477.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTD8
#15: Protein U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein / U4/U6.U5-27K / Nucleic acid-binding protein RY-1 / U4/U6.U5 tri-snRNP-associated 27 kDa protein / ...U4/U6.U5-27K / Nucleic acid-binding protein RY-1 / U4/U6.U5 tri-snRNP-associated 27 kDa protein / 27K / U4/U6.U5 tri-snRNP-associated protein 3


Mass: 18915.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WVK2
#23: 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: 95968.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15029
#24: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: Q9BUQ8, RNA helicase
#25: Protein
Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#29: Protein Pre-mRNA-processing factor 6


Mass: 97004.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q91YR7*PLUS
#30: Protein NHP2-like protein 1 / High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 ...High mobility group-like nuclear protein 2 homolog 1 / OTK27 / SNU13 homolog / hSNU13 / U4/U6.U5 small nuclear ribonucleoprotein SNU13 / U4/U6.U5 tri-snRNP 15.5 kDa protein


Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#36: Protein Pre-mRNA-processing-splicing factor 8 / 220 kDa U5 snRNP-specific protein / PRP8 homolog / Splicing factor Prp8 / p220


Mass: 271508.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P2Q9
#39: Protein Thioredoxin-like protein 4A / DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP ...DIM1 protein homolog / Spliceosomal U5 snRNP-specific 15 kDa protein / Thioredoxin-like U5 snRNP protein U5-15kD


Mass: 16807.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P83876
#41: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 11644.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0
#43: Protein Serine/threonine-protein kinase PRP4 homolog / PRP4 kinase / PRP4 pre-mRNA-processing factor 4 homolog


Mass: 117264.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13523, non-specific serine/threonine protein kinase

+
U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules 66676263686465

#14: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 9139.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62312
#18: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 11617.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UK45
#19: Protein U6 snRNA-associated Sm-like protein LSm2 / Protein G7b / Small nuclear ribonuclear protein D homolog / snRNP core Sm-like protein Sm-x5


Mass: 10847.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y333
#31: Protein U6 snRNA-associated Sm-like protein LSm3


Mass: 11859.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62310
#35: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 10410.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O95777
#40: Protein U6 snRNA-associated Sm-like protein LSm4 / Glycine-rich protein / GRP


Mass: 15375.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4Z0
#48: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 9945.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y4Y9

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules 2B2A

#20: Protein U2 small nuclear ribonucleoprotein B'' / U2 snRNP B''


Mass: 25524.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08579
#46: Protein U2 small nuclear ribonucleoprotein A' / U2 snRNP A'


Mass: 28456.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09661

+
Splicing factor 3A subunit ... , 3 types, 3 molecules A2A3A1

#21: Protein Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 24340.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428
#37: Protein Splicing factor 3A subunit 3 / SF3a60 / Spliceosome-associated protein 61 / SAP 61


Mass: 58934.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12874
#47: Protein Splicing factor 3A subunit 1,Splicing factor 3A subunit 1,Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 71619.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459

+
U4/U6.U5 tri-snRNP-associated protein ... , 2 types, 2 molecules SU

#28: Protein U4/U6.U5 tri-snRNP-associated protein 1 / SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / hSART-1 / U4/U6. ...SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / hSART-1 / U4/U6.U5 tri-snRNP-associated 110 kDa protein


Mass: 90414.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43290
#38: Protein U4/U6.U5 tri-snRNP-associated protein 2 / Inactive ubiquitin-specific peptidase 39 / SAD1 homolog / U4/U6.U5 tri-snRNP-associated 65 kDa protein / 65K


Mass: 64408.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q53GS9

+
Non-polymers , 4 types, 9 molecules

#51: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Zn
#52: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#53: 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
#54: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

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Experimental details

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Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Fully-assembled precatalytic spliceosome (pre-B complex).COMPLEX#1-#500MULTIPLE SOURCES
2Fully-assembled precatalytic spliceosome (pre-B complex).COMPLEX#1-#7, #9-#14, #16, #18-#23, #27-#50, #25-#26, #15, #171NATURAL
3Probable ATP-dependent RNA helicase DDX23COMPLEX#241RECOMBINANT
4AdML pre-mRNACOMPLEX#81RECOMBINANT
Molecular weightValue: 3.0 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Human adenovirus 210515
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Saccharomyces cerevisiae (brewer's yeast)4932
24synthetic construct (others)32630
Buffer solutionpH: 7.9
Buffer component
IDConc.NameBuffer-ID
120 mMHepes KOH1
250 mMKCl1
31 mMDTT1
40.2 mMEDTA1
SpecimenConc.: 1.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
2Gautomatchparticle selection
3EPUimage acquisition
5GctfCTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1130953
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86146 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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