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- PDB-8qzs: Cryo-EM structure of the cross-exon B-like complex -

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Basic information

Entry
Database: PDB / ID: 8qzs
TitleCryo-EM structure of the cross-exon B-like complex
Components
  • (Small nuclear ribonucleoprotein ...) 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
  • Microfibrillar-associated protein 1
  • NHP2-like protein 1, N-terminally processed
  • Oligo 1
  • Oligo 2
  • PHD finger-like domain-containing protein 5A
  • Peptidyl-prolyl cis-trans isomerase H
  • Pre-mRNA
  • Pre-mRNA-processing factor 6
  • Pre-mRNA-processing-splicing factor 8
  • Pre-mRNA-splicing factor 38A
  • Protein Red
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Thioredoxin-like protein 4A
  • U2 snRNA
  • U4 snRNA
  • U4/U6.U5 tri-snRNP-associated protein 1
  • U5 snRNA
  • U6 snRNA
  • Ubiquitin carboxyl-terminal hydrolase 39
  • WD40 repeat-containing protein SMU1
  • WW domain-binding protein 4
  • Zinc finger matrin-type protein 2
KeywordsSPLICING / spliceosome
Function / homology
Function and homology information


microfibril / 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 / U4atac snRNA binding ...microfibril / 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 / U4atac snRNA binding / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / U11/U12 snRNP / box C/D sno(s)RNA binding / PH domain binding / U2 snRNP binding / U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / dense fibrillar component / 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) / B-WICH complex / box C/D methylation guide snoRNP complex / protein methylation / U4/U6 snRNP / U12-type spliceosomal complex / protein localization to kinetochore / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / RNA splicing, via transesterification reactions / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / snRNP binding / blastocyst formation / sno(s)RNA-containing ribonucleoprotein complex / splicing factor binding / SMN-Sm protein complex / small nuclear ribonucleoprotein complex / proline-rich region binding / spliceosomal tri-snRNP complex / U4 snRNA binding / P granule / telomerase holoenzyme complex / U2-type precatalytic spliceosome / commitment complex / mRNA cis splicing, via spliceosome / telomerase RNA binding / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / box C/D snoRNP assembly / SAGA complex / RNA Polymerase II Transcription Termination / P-body assembly / U2 snRNP / U1 snRNP / U4 snRNP / U2-type prespliceosome / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / tRNA processing / positive regulation of transcription by RNA polymerase III / K63-linked polyubiquitin modification-dependent protein binding / cyclosporin A binding / precatalytic spliceosome / regulation of alternative mRNA splicing, via spliceosome / mitotic spindle assembly checkpoint signaling / regulation of RNA splicing / mRNA catabolic process / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / mRNA 3'-splice site recognition / positive regulation of transcription by RNA polymerase I / nuclear-transcribed mRNA catabolic process / MLL1 complex / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / protein deubiquitination / U5 snRNP / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal snRNP assembly / ribonucleoprotein complex binding / positive regulation of viral genome replication / RNA processing / U1 snRNA binding / Cajal body / regulation of DNA repair / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway
Similarity search - Function
Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / WD40 repeat-containing protein SMU1 / WW domain-binding protein 4 / Pre-mRNA-splicing factor 38, C-terminal / Pre-mRNA-splicing factor 38-associated hydrophilic C-term / Micro-fibrillar-associated protein 1, C-terminal ...Protein RED, C-terminal / RED-like, N-terminal / Protein Red-like / RED-like protein C-terminal region / RED-like protein N-terminal region / WD40 repeat-containing protein SMU1 / WW domain-binding protein 4 / 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 / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / : / LisH-like dimerisation domain / Pre-mRNA-splicing factor 38 / PRP38 family / USP39 / PRP4-like superfamily / pre-mRNA processing factor 4 (PRP4) like / C-terminal to LisH motif. / U1-C, C2H2-type zinc finger / U1 zinc finger / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / SF3B6, RNA recognition motif / 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 / 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 / U6 snRNA-associated Sm-like protein Lsm1/8 / 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 / SF3a60/Prp9 C-terminal / Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 / SF3B4, RNA recognition motif 1 / : / Splicing factor 3A subunit 1, conserved domain / Splicing factor 3A subunit 1 / Pre-mRNA splicing factor PRP21 like protein / : / : / Domain of unknown function DUF382 / Domain of unknown function (DUF382) / SWAP/Surp / Splicing factor 3B, subunit 5 / 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 / Zinc-finger of C2H2 type / : / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / : / Matrin/U1-C, C2H2-type zinc finger / : / Zinc finger matrin-type profile.
Similarity search - Domain/homology
: / : / : / : / 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 ...: / : / : / : / 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 / Protein Red / 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 / Ubiquitin carboxyl-terminal hydrolase 39 / 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 / 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: 4.1 Å
AuthorsZhang, Z. / Kumar, V. / Dybkov, O. / Will, C.L. / Zhong, J. / Ludwig, S. / Urlaub, H. / Kastner, B. / Stark, H. / Luehrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nature / Year: 2024
Title: Structural insights into the cross-exon to cross-intron spliceosome switch.
Authors: Zhenwei Zhang / Vinay Kumar / Olexandr Dybkov / Cindy L Will / Jiayun Zhong / Sebastian E J Ludwig / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur ...Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron. Alternatively, it can occur through an exon-defined pathway, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex. Exon definition promotes the splicing of upstream introns and plays a key part in alternative splicing regulation. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.
History
DepositionOct 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 10, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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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
5: U5 snRNA
2: U2 snRNA
6: U6 snRNA
4: U4 snRNA
C: 116 kDa U5 small nuclear ribonucleoprotein component
D: Thioredoxin-like protein 4A
E: U5 small nuclear ribonucleoprotein 40 kDa protein
I: Pre-mRNA-splicing factor 38A
M: NHP2-like protein 1, N-terminally processed
U: Ubiquitin carboxyl-terminal hydrolase 39
W: Peptidyl-prolyl cis-trans isomerase H
X: WW domain-binding protein 4
Z: Pre-mRNA
7: Splicing factor 3A subunit 1
r: Zinc finger matrin-type protein 2
B4: Splicing factor 3B subunit 4
8: Splicing factor 3A subunit 2
9: Splicing factor 3A subunit 3
B2: Splicing factor 3B subunit 2
B5: Splicing factor 3B subunit 5
B3: Splicing factor 3B subunit 3
BP: PHD finger-like domain-containing protein 5A
B1: Splicing factor 3B subunit 1
B6: Splicing factor 3B subunit 6
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
42: Small nuclear ribonucleoprotein Sm D2
4f: Small nuclear ribonucleoprotein F
4e: Small nuclear ribonucleoprotein E
4g: Small nuclear ribonucleoprotein G
43: Small nuclear ribonucleoprotein Sm D3
4b: Small nuclear ribonucleoprotein-associated proteins B and B'
41: Small nuclear ribonucleoprotein Sm D1
5e: Small nuclear ribonucleoprotein E
53: Small nuclear ribonucleoprotein Sm D3
5f: Small nuclear ribonucleoprotein F
51: Small nuclear ribonucleoprotein Sm D1
5b: Small nuclear ribonucleoprotein-associated proteins B and B'
52: Small nuclear ribonucleoprotein Sm D2
5g: Small nuclear ribonucleoprotein G
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'
x: Protein Red
y: Protein Red
w: WD40 repeat-containing protein SMU1
v: WD40 repeat-containing protein SMU1
K: Microfibrillar-associated protein 1
z1: Oligo 1
z2: Oligo 2
J: U4/U6 small nuclear ribonucleoprotein Prp3
L: U4/U6 small nuclear ribonucleoprotein Prp31
F: U4/U6 small nuclear ribonucleoprotein Prp4
N: Pre-mRNA-processing factor 6
S: U4/U6.U5 tri-snRNP-associated protein 1


Theoretical massNumber of molelcules
Total (without water)2,840,18568
Polymers2,840,18568
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 16 types, 20 molecules ACDIMUWXrBP4b5b2bxywvKNS

#1: 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
#7: 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
#8: 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
#10: 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
#11: Protein NHP2-like protein 1, N-terminally processed


Mass: 14191.524 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55769
#12: Protein Ubiquitin carboxyl-terminal hydrolase 39


Mass: 65481.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q53GS9
#13: 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
#14: 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
#17: 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
#24: 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
#39: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P14678
#43: 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
#44: 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
#45: 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
#51: 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
#52: 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

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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 / U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein ...U5-40K / 38 kDa-splicing factor / Prp8-binding protein / hPRP8BP / U5 snRNP-specific 40 kDa protein / WD repeat-containing protein 57


Mass: 39359.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96DI7

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RNA chain , 7 types, 7 molecules 5264Zz1z2

#3: 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
#4: RNA chain U2 snRNA


Mass: 60170.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 36516
#5: 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 U4 snRNA


Mass: 46181.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 340142
#15: RNA chain Pre-mRNA


Mass: 4714.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#46: RNA chain Oligo 1


Mass: 3555.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#47: RNA chain Oligo 2


Mass: 1303.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Splicing factor 3A subunit ... , 3 types, 3 molecules 789

#16: 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
#19: 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
#20: 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 B4B2B5B3B1B6

#18: 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
#21: 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
#22: 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
#23: 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
#25: 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
#26: 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

#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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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Small nuclear ribonucleoprotein ... , 6 types, 18 molecules 4252224f5f2f4e5e2e4g5g2g435323415121

#34: 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
#35: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein 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
#36: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein 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
#37: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein 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
#38: 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
#40: 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

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

#41: 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
#42: 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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U4/U6 small nuclear ribonucleoprotein ... , 3 types, 3 molecules JLF

#48: 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
#49: 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
#50: 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

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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: human spliceosomal cross-exon B-like complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334084 / Symmetry type: POINT

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