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- PDB-8h6k: Cryo-EM structure of human exon-defined spliceosome in the mature... -

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Basic information

Entry
Database: PDB / ID: 8h6k
TitleCryo-EM structure of human exon-defined spliceosome in the mature B state.
Components
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U4/U6 small nuclear ribonucleoprotein ...) x 3
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B'
  • Microfibrillar-associated protein 1
  • NHP2-like protein 1
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase H
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Pre-mRNA-splicing factor 38A
  • Thioredoxin-like protein 4A
  • U2 snRNAU2 spliceosomal RNA
  • U4 snRNAU4 spliceosomal RNA
  • U4/U6.U5 tri-snRNP-associated protein 1
  • U5 snRNAU5 spliceosomal RNA
  • U6 snRNAU6 spliceosomal RNA
  • Ubiquitin-like protein 5
  • WD40 repeat-containing protein SMU1
  • WW domain-binding protein 4
  • Zinc finger matrin-type protein 2
  • pre-mRNAPrimary transcript
KeywordsSPLICING / Exon-defined spliceosome / Post pre-B state
Function / homology
Function and homology information


spliceosomal snRNP complex / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding ...spliceosomal snRNP complex / microfibril / Lsm2-8 complex / U6 snRNA 3'-end binding / ribonucleoprotein complex localization / U4atac snRNP / positive regulation of cytotoxic T cell differentiation / maturation of 5S rRNA / RNA localization / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U11/U12 snRNP / box C/D sno(s)RNA binding / snRNP binding / U6 snRNP / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / dense fibrillar component / 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 / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / protein methylation / U4/U6 snRNP / U12-type spliceosomal complex / methylosome / P-body assembly / 7-methylguanosine cap hypermethylation / U2-type catalytic step 1 spliceosome / U1 snRNP binding / pICln-Sm protein complex / RNA splicing, via transesterification reactions / blastocyst formation / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / P granule / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / telomerase RNA binding / U2-type precatalytic spliceosome / positive regulation of mRNA splicing, via spliceosome / : / telomerase holoenzyme complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / box C/D snoRNP assembly / U4 snRNP / proline-rich region binding / rRNA modification in the nucleus and cytosol / U2 snRNP / SAGA complex / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process / positive regulation of transcription by RNA polymerase III / U1 snRNP / U3 snoRNA binding / U2-type prespliceosome / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of protein targeting to mitochondrion / tRNA processing / precatalytic spliceosome / cyclosporin A binding / regulation of alternative mRNA splicing, via spliceosome / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / mRNA Splicing - Minor Pathway / single fertilization / mRNA catabolic process / regulation of RNA splicing / MLL1 complex / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / U5 snRNA binding / U5 snRNP / positive regulation of viral genome replication / Cajal body / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / RNA processing / regulation of DNA repair / ribonucleoprotein complex binding / protein peptidyl-prolyl isomerization / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex
Similarity search - Function
WW domain-binding protein 4 / WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Ubiquitin-like modifier Hub1/Ubl5 / Microfibril-associated/Pre-mRNA processing / PRP4-like superfamily ...WW domain-binding protein 4 / WD40 repeat-containing protein SMU1 / LisH-like dimerisation domain / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal / Microfibrillar-associated protein 1 / Ubiquitin-like modifier Hub1/Ubl5 / Microfibril-associated/Pre-mRNA processing / PRP4-like superfamily / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / pre-mRNA processing factor 4 (PRP4) like / Pre-mRNA-splicing factor 38 / PRP38 family / SNU66/SART1 family / HIND motif / SART-1 family / HIND motif / PWI domain superfamily / PWI domain / PWI domain profile. / U1-C, C2H2-type zinc finger / U1 zinc finger / SF3B6, RNA recognition motif / Splicing factor 3A subunit 1, ubiquitin domain / SF3B4, RNA recognition motif 2 / C-terminal to LisH motif. / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Pre-mRNA processing factor 4 (PRP4)-like / Splicing Factor Motif, present in Prp18 and Pr04 / Prp31 C-terminal / U4/U6 small nuclear ribonucleoprotein Prp31 / Prp31 C terminal domain / Pre-mRNA-splicing factor 3 / U4/U6 small nuclear ribonucleoprotein Prp3 / Sm-like protein Lsm8 / pre-mRNA processing factor 3 domain / : / Replication stress response SDE2 C-terminal / Cactus-binding C-terminus of cactin protein / Small nuclear ribonucleoprotein Prp3, C-terminal domain / Small nuclear ribonucleoprotein Prp3, C-terminal domain / PWI domain / PWI, domain in splicing factors / U6 snRNA-associated Sm-like protein Lsm1/8 / Dim1 family / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Mitosis protein DIM1 / Mitosis protein DIM1 / Sm-like protein Lsm7 / PRP1 splicing factor, N-terminal / Sm-like protein LSm5 / Sm-like protein Lsm3 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / U6 snRNA-associated Sm-like protein Lsm3 / PRP1 splicing factor, N-terminal / Splicing factor 3A subunit 1 / Splicing factor 3A subunit 1, conserved domain / Pre-mRNA splicing factor PRP21 like protein / SF3A2 domain / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3B4, RNA recognition motif 1 / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Splicing factor 3B, subunit 5 / SWAP/Surp / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / 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) / Small ribonucleoprotein associated, SmB/SmN / Splicing factor 3B subunit 1-like / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / Lissencephaly type-1-like homology motif / Small nuclear ribonucleoprotein D1 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-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 ...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 / Peptidyl-prolyl cis-trans isomerase H / Splicing factor 3B subunit 1 / WW domain-binding protein 4 / U5 small nuclear ribonucleoprotein 200 kDa helicase / Pre-mRNA-processing factor 6 / U6 snRNA-associated Sm-like protein LSm8 / U2 small nuclear ribonucleoprotein B'' / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein-associated proteins B and B' / Microfibrillar-associated protein 1 / 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 / 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 / WD40 repeat-containing protein SMU1 / Pre-mRNA-processing-splicing factor 8 / PHD finger-like domain-containing protein 5A / Pre-mRNA-splicing factor 38A / U4/U6 small nuclear ribonucleoprotein Prp31 / U5 small nuclear ribonucleoprotein 40 kDa protein / Zinc finger matrin-type protein 2 / Splicing factor 3B subunit 5 / Ubiquitin-like protein 5 / U6 snRNA-associated Sm-like protein LSm7 / U6 snRNA-associated Sm-like protein LSm2 / Splicing factor 3B subunit 6 / U6 snRNA-associated Sm-like protein LSm5 / U6 snRNA-associated Sm-like protein LSm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhang, W. / Zhan, X. / Zhang, X. / Bai, R. / Lei, J. / Yan, C. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Res / Year: 2024
Title: Structural insights into human exon-defined spliceosome prior to activation.
Authors: Wenyu Zhang / Xiaofeng Zhang / Xiechao Zhan / Rui Bai / Jianlin Lei / Chuangye Yan / Yigong Shi /
Abstract: Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, ...Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.
History
DepositionOct 18, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pre-mRNA
5A: U5 snRNA
5B: Pre-mRNA-processing-splicing factor 8
5C: 116 kDa U5 small nuclear ribonucleoprotein component
5D: U5 small nuclear ribonucleoprotein 200 kDa helicase
5E: U5 small nuclear ribonucleoprotein 40 kDa protein
5a: Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B'
5b: Small nuclear ribonucleoprotein Sm D1
5c: Small nuclear ribonucleoprotein Sm D2
5d: Small nuclear ribonucleoprotein F
5e: Small nuclear ribonucleoprotein E
5f: Small nuclear ribonucleoprotein G
5g: Small nuclear ribonucleoprotein Sm D3
6A: U6 snRNA
6a: U6 snRNA-associated Sm-like protein LSm2
6b: U6 snRNA-associated Sm-like protein LSm3
6c: U6 snRNA-associated Sm-like protein LSm4
6d: U6 snRNA-associated Sm-like protein LSm5
6e: U6 snRNA-associated Sm-like protein LSm6
6f: U6 snRNA-associated Sm-like protein LSm7
6g: U6 snRNA-associated Sm-like protein LSm8
4A: U4 snRNA
4B: U4/U6 small nuclear ribonucleoprotein Prp3
4C: U4/U6 small nuclear ribonucleoprotein Prp4
4D: U4/U6 small nuclear ribonucleoprotein Prp31
4E: NHP2-like protein 1
4F: Thioredoxin-like protein 4A
4G: Pre-mRNA-processing factor 6
4H: Peptidyl-prolyl cis-trans isomerase H
4I: WW domain-binding protein 4
4J: U4/U6.U5 tri-snRNP-associated protein 1
4K: Microfibrillar-associated protein 1
4L: Pre-mRNA-splicing factor 38A
4M: Ubiquitin-like protein 5
4N: Zinc finger matrin-type protein 2
4Z: WD40 repeat-containing protein SMU1
4a: Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B'
4b: Small nuclear ribonucleoprotein Sm D1
4c: Small nuclear ribonucleoprotein Sm D2
4d: Small nuclear ribonucleoprotein F
4e: Small nuclear ribonucleoprotein E
4f: Small nuclear ribonucleoprotein G
4g: Small nuclear ribonucleoprotein Sm D3
2A: U2 snRNA
2B: U2 small nuclear ribonucleoprotein A'
2C: U2 small nuclear ribonucleoprotein B''
2D: Splicing factor 3A subunit 1
2E: Splicing factor 3A subunit 2
2F: Splicing factor 3A subunit 3
2G: Splicing factor 3B subunit 1
2H: Splicing factor 3B subunit 2
2I: Splicing factor 3B subunit 3
2J: Splicing factor 3B subunit 4
2K: Splicing factor 3B subunit 6
2L: PHD finger-like domain-containing protein 5A
2M: Splicing factor 3B subunit 5
2a: Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B'
2b: Small nuclear ribonucleoprotein Sm D1
2c: Small nuclear ribonucleoprotein Sm D2
2d: Small nuclear ribonucleoprotein F
2e: Small nuclear ribonucleoprotein E
2f: Small nuclear ribonucleoprotein G
2g: Small nuclear ribonucleoprotein Sm D3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,629,83368
Polymers2,628,49563
Non-polymers1,3385
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 5 types, 5 molecules A5A6A4A2A

#1: RNA chain pre-mRNA / Primary transcript


Mass: 45960.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: RNA chain U5 snRNA / U5 spliceosomal RNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#14: RNA chain U6 snRNA / U6 spliceosomal RNA


Mass: 34404.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#22: RNA chain U4 snRNA / U4 spliceosomal RNA


Mass: 46650.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#37: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516

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Protein , 15 types, 17 molecules 5B5C5a4a2a4E4F4G4H4I4J4K4L4M4N4Z2L

#3: 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
#7: Protein Isoform SM-B of Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / Sm-B/B' / SmB/B'


Mass: 23686.004 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#26: 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
#27: 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
#28: 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
#29: Protein Peptidyl-prolyl cis-trans isomerase H / PPIase H / Rotamase H / Small nuclear ribonucleoprotein particle-specific cyclophilin H / CypH / U- ...PPIase H / Rotamase H / Small nuclear ribonucleoprotein particle-specific cyclophilin H / CypH / U-snRNP-associated cyclophilin SnuCyp-20 / USA-CYP


Mass: 19230.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43447, peptidylprolyl isomerase
#30: Protein WW domain-binding protein 4 / WBP-4 / Formin-binding protein 21 / WW domain-containing-binding protein 4


Mass: 42575.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75554
#31: Protein U4/U6.U5 tri-snRNP-associated protein 1 / SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-1 / hSART-1 ...SNU66 homolog / hSnu66 / Squamous cell carcinoma antigen recognized by T-cells 1 / SART-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
#32: Protein Microfibrillar-associated protein 1 / Spliceosome B complex protein MFAP1


Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55081
#33: Protein Pre-mRNA-splicing factor 38A


Mass: 37563.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NAV1
#34: Protein Ubiquitin-like protein 5


Mass: 8560.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZL1
#35: Protein Zinc finger matrin-type protein 2


Mass: 23664.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96NC0
#36: Protein WD40 repeat-containing protein SMU1 / Smu-1 suppressor of mec-8 and unc-52 protein homolog


Mass: 57616.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TAY7
#48: Protein PHD finger-like domain-containing protein 5A / PHD finger-like domain protein 5A / Splicing factor 3B-associated 14 kDa protein / SF3b14b


Mass: 12427.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7RTV0

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U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules 5D5E

#5: 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
#6: Protein U5 small nuclear ribonucleoprotein 40 kDa protein / U5 snRNP 40 kDa protein / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 ...U5 snRNP 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, 18 molecules 5b4b2b5c4c2c5d4d2d5e4e2e5f4f2f5g4g2g

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


Mass: 13310.653 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314
#9: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#10: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / Sm-F / SmF


Mass: 9734.171 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#11: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 10817.601 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#12: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8508.084 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#13: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318

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U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules 6a6b6c6d6e6f6g

#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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

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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules 4B4C4D

#23: 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
#24: 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
#25: 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 / Protein 61K / hPrp31


Mass: 55528.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WWY3

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U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules 2B2C

#38: 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
#39: 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

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Splicing factor 3A subunit ... , 3 types, 3 molecules 2D2E2F

#40: Protein Splicing factor 3A subunit 1 / SF3a120 / Spliceosome-associated protein 114 / SAP 114


Mass: 88991.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15459
#41: Protein Splicing factor 3A subunit 2 / SF3a66 / Spliceosome-associated protein 62 / SAP 62


Mass: 49327.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15428
#42: 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

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Splicing factor 3B subunit ... , 6 types, 6 molecules 2G2H2I2J2K2M

#43: 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
#44: 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
#45: 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
#46: 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
#47: Protein Splicing factor 3B subunit 6 / Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / ...Pre-mRNA branch site protein p14 / SF3b 14 kDa subunit / SF3B14a / Spliceosome-associated protein / 14-kDa / Splicing factor 3b / subunit 6 / 14kDa


Mass: 14606.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y3B4
#49: 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

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Non-polymers , 4 types, 5 molecules

#50: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#51: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#53: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: exon-defined post pre-B spliceosome / Type: COMPLEX / Entity ID: #2-#15, #17, #20, #22-#36 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414060 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00351962
ELECTRON MICROSCOPYf_angle_d0.60271419
ELECTRON MICROSCOPYf_dihedral_angle_d10.6018907
ELECTRON MICROSCOPYf_chiral_restr0.0398117
ELECTRON MICROSCOPYf_plane_restr0.0048466

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