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- PDB-9r8v: Cryo-EM structure of the human pre-Bact-OTS complex (whole map) -

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Basic information

Entry
Database: PDB / ID: 9r8v
TitleCryo-EM structure of the human pre-Bact-OTS complex (whole map)
Components
  • (Pre-mRNA-splicing factor ...) x 2
  • (Small nuclear ribonucleoprotein ...) x 6
  • (Splicing factor 3A subunit ...) x 3
  • (Splicing factor 3B subunit ...) x 6
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • (U5 small nuclear ribonucleoprotein ...) x 2
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • 116 kDa U5 small nuclear ribonucleoprotein component
  • ATP-dependent RNA helicase DHX15
  • Beta-catenin-like protein 1
  • Cell division cycle 5-like protein
  • Microfibrillar-associated protein 1
  • PHD finger-like domain-containing protein 5A
  • Pleiotropic regulator 1
  • Pre-mRNA-processing factor 17
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • Protein Red
  • RING-type E3 ubiquitin-protein ligase PPIL2
  • SNW domain-containing protein 1
  • Serine/arginine-rich splicing factor 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • Transcription elongation regulator 1
  • U2 snRNA
  • U2 snRNP-associated SURP motif-containing protein
  • U5 snRNA
  • U6 snRNA
  • Ubiquitin-like protein 5
  • WD40 repeat-containing protein SMU1
  • WW domain-binding protein 11
  • Zinc finger matrin-type protein 2
  • pre-mRNA
KeywordsSPLICING / spliceosome
Function / homology
Function and homology information


protein localization to P-body / DNA topoisomerase binding / RS domain binding / microfibril / Lsm2-8 complex / somatic diversification of immunoglobulins / U6 snRNA 3'-end binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / protein kinase B binding ...protein localization to P-body / DNA topoisomerase binding / RS domain binding / microfibril / Lsm2-8 complex / somatic diversification of immunoglobulins / U6 snRNA 3'-end binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / protein kinase B binding / U6 snRNP / PH domain binding / U11/U12 snRNP / regulation of retinoic acid receptor signaling pathway / interleukin-17-mediated signaling pathway / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / cis assembly of pre-catalytic spliceosome / histone pre-mRNA 3'end processing complex / regulation of vitamin D receptor signaling pathway / mRNA splice site recognition / 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) / B-WICH complex / alternative mRNA splicing, via spliceosome / protein localization to kinetochore / protein methylation / 7-methylguanosine cap hypermethylation / U12-type spliceosomal complex / nuclear retinoic acid receptor binding / embryonic brain development / U1 snRNP binding / U2-type catalytic step 1 spliceosome / methylosome / pICln-Sm protein complex / ATP-dependent activity, acting on RNA / response to alkaloid / RNA splicing, via transesterification reactions / positive regulation of mRNA splicing, via spliceosome / signal transduction involved in regulation of gene expression / mRNA 3'-end processing / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / splicing factor binding / blastocyst formation / P granule / positive regulation of vitamin D receptor signaling pathway / snRNP binding / commitment complex / host-mediated activation of viral transcription / U2-type precatalytic spliceosome / mRNA cis splicing, via spliceosome / telomerase holoenzyme complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RNA polymerase binding / Notch binding / RUNX3 regulates NOTCH signaling / telomerase RNA binding / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / U2-type spliceosomal complex / nuclear vitamin D receptor binding / NOTCH4 Intracellular Domain Regulates Transcription / transcription elongation factor activity / U1 snRNP / SAGA complex / U2 snRNP / RNA Polymerase II Transcription Termination / U4 snRNP / P-body assembly / NOTCH3 Intracellular Domain Regulates Transcription / : / U2-type prespliceosome / tRNA processing / Basigin interactions / mRNA stabilization / positive regulation of transcription by RNA polymerase III / positive regulation of neurogenesis / nuclear androgen receptor binding / ubiquitin-ubiquitin ligase activity / precatalytic spliceosome / Notch-HLH transcription pathway / WW domain binding / ubiquitin-like protein conjugating enzyme binding / Formation of paraxial mesoderm / mitotic spindle assembly checkpoint signaling / WD40-repeat domain binding / regulation of alternative mRNA splicing, via spliceosome / mRNA 5'-splice site recognition / positive regulation of transforming growth factor beta receptor signaling pathway / mRNA 3'-splice site recognition / SMAD binding / regulation of RNA splicing / mRNA catabolic process
Similarity search - Function
: / SR140, RNA recognition motif / WW domain binding protein 11 / WW domain binding protein 11 / Protein RED, C-terminal / RED-like, N-terminal / Beta-catenin-like protein 1, N-terminal / Beta-catenin-like protein 1 / Protein Red-like / RED-like protein C-terminal region ...: / SR140, RNA recognition motif / WW domain binding protein 11 / WW domain binding protein 11 / Protein RED, C-terminal / RED-like, N-terminal / Beta-catenin-like protein 1, N-terminal / Beta-catenin-like protein 1 / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / Catenin-beta-like, Arm-motif containing nuclear / Eukaryotic domain of unknown function (DUF1716) / : / SRSF1, RNA recognition motif 1 / : / WD40 repeat-containing protein SMU1 / Peptidyl-prolyl cis-trans isomerase like 2, U-box domain / Ubiquitin-like modifier Hub1/Ubl5 / 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 / Microfibril-associated/Pre-mRNA processing / DHX15, DEXH-box helicase domain / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / Transcription elongation regulator 1-like / : / PRP38 family / TCERG1 WW domain / : / LisH-like dimerisation domain / cwf21 / FF domain / C-terminal to LisH motif. / CID domain / RPR / FF domain / CID domain / FF domain superfamily / CID domain profile. / FF domain profile. / Contains two conserved F residues / Sm-like protein Lsm8 / CTLH, C-terminal LisH motif / SF3B6, RNA recognition motif / C-terminal to LisH (CTLH) motif profile. / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SF3B4, RNA recognition motif 2 / Splicing factor SF3a60 binding domain / Splicing factor SF3a60 binding domain / Cactus-binding C-terminus of cactin protein / Splicing factor 3A subunit 1, ubiquitin domain / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 / U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 / : / Replication stress response SDE2 C-terminal / mRNA splicing factor Cwf21 domain / cwf21 domain / SF3A2 domain / : / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / Splicing factor SF3a60 /Prp9 subunit, C-terminal / SF3A3 domain / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / Pre-mRNA-processing factor 17 / SF3B4, RNA recognition motif 1 / : / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / G10 protein signature 2. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / : / BUD31/G10-related, conserved site / : / G10 protein signature 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 / Splicing factor 3B, subunit 5 / SKI-interacting protein SKIP, SNW domain / Pre-mRNA-splicing factor Cwf15/Cwc15 / SKI-interacting protein, SKIP / SKIP/SNW domain / Cwf15/Cwc15 cell cycle control protein / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / Transcription elongation regulator 1 / U2 snRNP-associated SURP motif-containing protein / ATP-dependent RNA helicase DHX15 / Pleiotropic regulator 1 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / Transcription elongation regulator 1 / U2 snRNP-associated SURP motif-containing protein / ATP-dependent RNA helicase DHX15 / Pleiotropic regulator 1 / Pre-mRNA-processing factor 17 / Splicing factor 3B subunit 1 / U5 small nuclear ribonucleoprotein 200 kDa helicase / 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' / Protein BUD31 homolog / Microfibrillar-associated 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 / Serine/arginine-rich splicing factor 1 / Splicing factor 3A subunit 3 / Protein Red / RING-type E3 ubiquitin-protein ligase PPIL2 / Splicing factor 3B subunit 2 / SNW domain-containing protein 1 / 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 / PHD finger-like domain-containing protein 5A / Pre-mRNA-splicing factor 38A / Beta-catenin-like protein 1 / U5 small nuclear ribonucleoprotein 40 kDa protein / Zinc finger matrin-type protein 2 / Cell division cycle 5-like protein / Splicing factor 3B subunit 5 / Ubiquitin-like protein 5 / Spliceosome-associated protein CWC15 homolog / U6 snRNA-associated Sm-like protein LSm7 / WW domain-binding protein 11 / 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: 8.5 Å
AuthorsZhang, Z. / Kumar, V. / Zhong, J. / Dybkov, O. / Kastner, B. / Urlaub, H. / Luhrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: To Be Published
Title: cryo-EM structure of the human pre-Bact-OTS complex
Authors: Zhang, Z. / Kumar, V. / Dybkov, O. / Zhong, J. / Kastner, B. / Henning, U. / Luehrmann, R.
History
DepositionMay 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-processing-splicing factor 8
B: U5 small nuclear ribonucleoprotein 200 kDa helicase
2: U2 snRNA
6: U6 snRNA
7: Splicing factor 3A subunit 1
5: U5 snRNA
L: Cell division cycle 5-like protein
C: 116 kDa U5 small nuclear ribonucleoprotein component
E: U5 small nuclear ribonucleoprotein 40 kDa protein
G: Pleiotropic regulator 1
I: Pre-mRNA-splicing factor 38A
Q: Protein BUD31 homolog
R: Spliceosome-associated protein CWC15 homolog
X: WW domain-binding protein 11
q: Ubiquitin-like protein 5
r: Zinc finger matrin-type protein 2
22: Small nuclear ribonucleoprotein Sm D2
2B: U2 small nuclear ribonucleoprotein B''
2f: Small nuclear ribonucleoprotein F
2b: Small nuclear ribonucleoprotein-associated proteins B and B'
23: Small nuclear ribonucleoprotein Sm D3
2g: Small nuclear ribonucleoprotein G
2e: Small nuclear ribonucleoprotein E
21: Small nuclear ribonucleoprotein Sm D1
2A: U2 small nuclear ribonucleoprotein A'
B4: Splicing factor 3B subunit 4
9: Splicing factor 3A subunit 3
8: Splicing factor 3A subunit 2
B2: Splicing factor 3B subunit 2
B5: Splicing factor 3B subunit 5
B3: Splicing factor 3B subunit 3
B1: Splicing factor 3B subunit 1
B6: Splicing factor 3B subunit 6
BL: Beta-catenin-like protein 1
SR: U2 snRNP-associated SURP motif-containing protein
DH: ATP-dependent RNA helicase DHX15
Z: pre-mRNA
x: Protein Red
y: Protein Red
v: WD40 repeat-containing protein SMU1
w: WD40 repeat-containing protein SMU1
P: Pre-mRNA-splicing factor RBM22
t: RING-type E3 ubiquitin-protein ligase PPIL2
5b: Small nuclear ribonucleoprotein-associated proteins B and B'
51: Small nuclear ribonucleoprotein Sm D1
52: Small nuclear ribonucleoprotein Sm D2
53: Small nuclear ribonucleoprotein Sm D3
5e: Small nuclear ribonucleoprotein E
5f: Small nuclear ribonucleoprotein F
5g: Small nuclear ribonucleoprotein G
62: U6 snRNA-associated Sm-like protein LSm2
63: U6 snRNA-associated Sm-like protein LSm3
64: U6 snRNA-associated Sm-like protein LSm4
65: U6 snRNA-associated Sm-like protein LSm5
66: U6 snRNA-associated Sm-like protein LSm6
67: U6 snRNA-associated Sm-like protein LSm7
68: U6 snRNA-associated Sm-like protein LSm8
S1: SNW domain-containing protein 1
A6: Serine/arginine-rich splicing factor 1
T: Transcription elongation regulator 1
K: Microfibrillar-associated protein 1
P7: Pre-mRNA-processing factor 17
5A: PHD finger-like domain-containing protein 5A


Theoretical massNumber of molelcules
Total (without water)3,268,15163
Polymers3,268,15163
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 22 types, 25 molecules ALCGQRXqr2b5bBLSRDHxyvwtS1A6TKP75A

#1: Protein Pre-mRNA-processing-splicing factor 8


Mass: 325927.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#7: Protein Cell division cycle 5-like protein / Cdc5-like protein / Pombe cdc5-related protein


Mass: 92406.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99459
#8: 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
#10: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43660
#12: Protein Protein BUD31 homolog / Protein EDG-2 / Protein G10 homolog


Mass: 17032.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41223
#13: Protein Spliceosome-associated protein CWC15 homolog


Mass: 26674.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9P013
#14: Protein WW domain-binding protein 11 / WBP-11 / Npw38-binding protein / NpwBP / SH3 domain-binding protein SNP70 / Splicing factor that ...WBP-11 / Npw38-binding protein / NpwBP / SH3 domain-binding protein SNP70 / Splicing factor that interacts with PQBP-1 and PP1


Mass: 70098.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y2W2
#15: 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
#16: 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
#20: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / Sm-B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#34: Protein Beta-catenin-like protein 1 / Nuclear-associated protein / NAP / Testis development protein NYD-SP19


Mass: 65264.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WYA6
#35: Protein U2 snRNP-associated SURP motif-containing protein / 140 kDa Ser/Arg-rich domain protein / U2-associated protein SR140


Mass: 118503.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15042
#36: Protein ATP-dependent RNA helicase DHX15 / ATP-dependent RNA helicase #46 / DEAH box protein 15 / Splicing factor Prp43 / hPrp43


Mass: 91065.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O43143, RNA helicase
#38: Protein Protein Red


Mass: 65731.508 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13123
#39: Protein WD40 repeat-containing protein SMU1 / Smu-1 suppressor of mec-8 and unc-52 protein homolog


Mass: 57616.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2TAY7
#41: Protein RING-type E3 ubiquitin-protein ligase PPIL2 / CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive ...CYC4 / Cyclophilin-60 / Cyclophilin-like protein Cyp-60 / Cyp60 / hCyP-60 / Probable inactive peptidyl-prolyl cis-trans isomerase-like 2 / PPIase / Rotamase PPIL2


Mass: 58910.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q13356, RING-type E3 ubiquitin transferase
#49: Protein SNW domain-containing protein 1 / Nuclear protein SkiP / Nuclear receptor coactivator NCoA-62 / Ski-interacting protein


Mass: 61610.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13573
#50: Protein Serine/arginine-rich splicing factor 1 / Alternative-splicing factor 1 / ASF-1 / Splicing factor / arginine/serine-rich 1 / pre-mRNA- ...Alternative-splicing factor 1 / ASF-1 / Splicing factor / arginine/serine-rich 1 / pre-mRNA-splicing factor SF2 / P33 subunit


Mass: 27798.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q07955
#51: Protein Transcription elongation regulator 1 / TATA box-binding protein-associated factor 2S / Transcription factor CA150


Mass: 124083.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O14776
#52: 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
#53: Protein Pre-mRNA-processing factor 17 / Cell division cycle 40 homolog / EH-binding protein 3 / Ehb3 / PRP17 homolog / hPRP17


Mass: 65612.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O60508
#54: 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 BE

#2: 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
#9: 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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RNA chain , 4 types, 4 molecules 265Z

#3: RNA chain U2 snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#4: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_004394.1
#6: RNA chain U5 snRNA


Mass: 37254.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 20330981
#37: RNA chain pre-mRNA


Mass: 132594.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PM5-10 pre-mRNA with MS2 loop / Source: (natural) Homo sapiens (human)

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Splicing factor 3A subunit ... , 3 types, 3 molecules 798

#5: 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
#27: 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
#28: 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

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Pre-mRNA-splicing factor ... , 2 types, 2 molecules IP

#11: 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
#40: Protein Pre-mRNA-splicing factor RBM22


Mass: 56285.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules 22522f5f23532g5g2e5e2151

#17: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 13551.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62316
#19: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9734.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62306
#21: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 13940.308 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62318
#22: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / Sm-G / SmG


Mass: 8508.084 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62308
#23: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / Sm-E / SmE


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62304
#24: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13310.653 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62314

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

#18: 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
#25: 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

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Splicing factor 3B subunit ... , 6 types, 6 molecules B4B2B5B3B1B6

#26: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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

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U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules 62636465666768

#42: 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
#43: 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
#44: 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
#45: 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
#46: 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
#47: 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
#48: 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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Details

Has protein modificationN

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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: OTS-stalled spliceosome complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: OTS-stalled spliceosome complex particles
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TITAN THEMIS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55345 / Symmetry type: POINT

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