[English] 日本語
Yorodumi
- PDB-7abg: Human pre-Bact-1 spliceosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7abg
TitleHuman pre-Bact-1 spliceosome
Components
  • (Nuclear cap-binding protein subunit ...) x 2
  • (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
  • Cell division cycle 5-like protein
  • MINX M3 pre-mRNA
  • Microfibrillar-associated protein 1
  • PHD finger-like domain-containing protein 5A
  • Pleiotropic regulator 1
  • Pre-mRNA-processing-splicing factor 8
  • Protein BUD31 homolog
  • SNW domain-containing protein 1
  • Serine/arginine repetitive matrix protein 1
  • Serine/arginine-rich splicing factor 1
  • Smad nuclear-interacting protein 1
  • Small nuclear ribonucleoprotein-associated proteins B and B'
  • Spliceosome-associated protein CWC15 homolog
  • Transcription elongation regulator 1
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • Ubiquitin-like protein 5
  • WW domain-binding protein 11
  • Zinc finger matrin-type protein 2
KeywordsSPLICING / Complex / spliceosome / catalytic activation
Function / homology
Function and homology information


protein localization to P-body / positive regulation of RNA binding / snRNA export from nucleus / DNA topoisomerase binding / RS domain binding / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / microfibril / mRNA metabolic process ...protein localization to P-body / positive regulation of RNA binding / snRNA export from nucleus / DNA topoisomerase binding / RS domain binding / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / microfibril / mRNA metabolic process / Lsm2-8 complex / U6 snRNA 3'-end binding / positive regulation of RNA export from nucleus / mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / protein kinase B binding / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / U6 snRNP / Processing of Intronless Pre-mRNAs / U11/U12 snRNP / PH domain binding / regulation of retinoic acid receptor signaling pathway / U2 snRNP binding / interleukin-17-mediated signaling pathway / U7 snRNA binding / histone pre-mRNA DCP binding / RNA cap binding / U7 snRNP / snRNA binding / histone pre-mRNA 3'end processing complex / cis assembly of pre-catalytic spliceosome / regulation of mRNA processing / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / 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) / regulatory ncRNA-mediated post-transcriptional gene silencing / B-WICH complex / miRNA processing / nuclear retinoic acid receptor binding / protein methylation / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / U12-type spliceosomal complex / Transport of the SLBP Dependant Mature mRNA / alternative mRNA splicing, via spliceosome / 7-methylguanosine cap hypermethylation / U1 snRNP binding / methylosome / mRNA 3'-end processing / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / RNA splicing, via transesterification reactions / snRNP binding / Transport of Mature mRNA Derived from an Intronless Transcript / pre-mRNA binding / regulation of mRNA splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / transcription elongation factor activity / blastocyst formation / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / SMN-Sm protein complex / splicing factor binding / spliceosomal tri-snRNP complex / Notch binding / host-mediated activation of viral transcription / mRNA 3'-end processing / P granule / mRNA stabilization / telomerase holoenzyme complex / U2-type precatalytic spliceosome / commitment complex / mRNA cis splicing, via spliceosome / positive regulation of vitamin D receptor signaling pathway / telomerase RNA binding / U2-type prespliceosome assembly / U2-type spliceosomal complex / nuclear vitamin D receptor binding / RNA polymerase binding / U2-type catalytic step 2 spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / RNA catabolic process / U2 snRNP / P-body assembly / signal transduction involved in regulation of gene expression / RNA Polymerase II Transcription Termination / SAGA complex / U1 snRNP / RHOBTB1 GTPase cycle / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / U4 snRNP
Similarity search - Function
WW domain binding protein 11 / WW domain binding protein 11 / : / SRSF1, RNA recognition motif 1 / : / 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 ...WW domain binding protein 11 / WW domain binding protein 11 / : / SRSF1, RNA recognition motif 1 / : / 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 / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / U4/U6.U5 small nuclear ribonucleoprotein component Snu23 / Pre-mRNA-splicing factor 38 / Transcription elongation regulator 1-like / PRP38 family / TCERG1 WW domain / FF domain / SF3B6, RNA recognition motif / : / FF domain / FF domain superfamily / FF domain profile. / Contains two conserved F residues / Sm-like protein Lsm8 / PWI domain superfamily / PWI domain / PWI domain profile. / SF3B4, RNA recognition motif 2 / U6 snRNA-associated Sm-like protein LSm2 / Splicing factor SF3a60 binding domain / Sm-like protein Lsm4 / Splicing factor SF3a60 binding domain / 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 / Splicing factor 3A subunit 1, ubiquitin domain / : / Replication stress response SDE2 C-terminal / PWI domain / PWI, domain in splicing factors / SF3A2 domain / : / 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) / G10 protein signature 2. / SWAP/Surp / Splicing factor 3B, subunit 5 / SWAP/Surp superfamily / Surp module / SURP motif repeat profile. / Suppressor-of-White-APricot splicing regulator / BUD31/G10-related, conserved site / G10 protein signature 1. / Splicing factor 3B subunit 1 / Splicing factor 3B subunit 1 / Zinc-finger of C2H2 type / : / STL11, N-terminal / SKI-interacting protein SKIP, SNW domain / PSP, proline-rich / SKI-interacting protein, SKIP / SKIP/SNW domain / PSP / proline-rich domain in spliceosome associated proteins / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / Matrin/U1-C, C2H2-type zinc finger / Zinc finger matrin-type profile. / G10 protein / Pre-mRNA-splicing factor BUD31 / PHF5-like / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / :
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Transcription elongation regulator 1 / Pleiotropic regulator 1 ...7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100) / Transcription elongation regulator 1 / Pleiotropic regulator 1 / 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 / Nuclear cap-binding protein subunit 2 / 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 / Nuclear cap-binding protein subunit 1 / Splicing factor 3A subunit 3 / 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 / Pre-mRNA-processing-splicing factor 8 / PHD finger-like domain-containing protein 5A / Serine/arginine repetitive matrix protein 1 / Pre-mRNA-splicing factor 38A / Smad nuclear-interacting 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 / Pre-mRNA-splicing factor RBM22 / 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)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsTownsend, C. / Kastner, B. / Leelaram, M.N. / Bertram, K. / Stark, H. / Luehrmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)860 Germany
CitationJournal: Science / Year: 2020
Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation.
Authors: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann /
Abstract: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway ...Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.
History
DepositionSep 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11695
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A5: Nuclear cap-binding protein subunit 1
A2: U6 snRNA-associated Sm-like protein LSm7
z: Splicing factor 3B subunit 6
F: Splicing factor 3A subunit 2
D: U5 small nuclear ribonucleoprotein 40 kDa protein
W: U2 small nuclear ribonucleoprotein A'
B: U2 small nuclear ribonucleoprotein B''
s: U5 small nuclear ribonucleoprotein 200 kDa helicase
Q: Protein BUD31 homolog
A1: Nuclear cap-binding protein subunit 2
5: U5 snRNA
L: Cell division cycle 5-like protein
R: Spliceosome-associated protein CWC15 homolog
V: U6 snRNA-associated Sm-like protein LSm2
9: U6 snRNA-associated Sm-like protein LSm3
C: U6 snRNA-associated Sm-like protein LSm4
H: U6 snRNA-associated Sm-like protein LSm5
J: U6 snRNA-associated Sm-like protein LSm6
2: U2 snRNA
A3: U6 snRNA-associated Sm-like protein LSm8
K: Microfibrillar-associated protein 1
y: PHD finger-like domain-containing protein 5A
G: Pleiotropic regulator 1
Z: MINX M3 pre-mRNA
A: Pre-mRNA-processing-splicing factor 8
I: Pre-mRNA-splicing factor 38A
P: Pre-mRNA-splicing factor RBM22
p: Splicing factor 3A subunit 1
4: Splicing factor 3A subunit 3
A4: Transcription elongation regulator 1
u: Splicing factor 3B subunit 1
T: Splicing factor 3B subunit 2
E: Splicing factor 3B subunit 3
w: Splicing factor 3B subunit 4
x: Splicing factor 3B subunit 5
v: SNW domain-containing protein 1
0: Smad nuclear-interacting protein 1
N: Zinc finger matrin-type protein 2
r: 116 kDa U5 small nuclear ribonucleoprotein component
Y: Serine/arginine repetitive matrix protein 1
6: U6 snRNA
A6: Serine/arginine-rich splicing factor 1
h: Small nuclear ribonucleoprotein Sm D2
i: Small nuclear ribonucleoprotein F
m: Small nuclear ribonucleoprotein-associated proteins B and B'
l: Small nuclear ribonucleoprotein Sm D3
k: Small nuclear ribonucleoprotein G
j: Small nuclear ribonucleoprotein E
n: Small nuclear ribonucleoprotein Sm D1
f: Small nuclear ribonucleoprotein-associated proteins B and B'
g: Small nuclear ribonucleoprotein Sm D1
a: Small nuclear ribonucleoprotein Sm D2
e: Small nuclear ribonucleoprotein Sm D3
c: Small nuclear ribonucleoprotein E
b: Small nuclear ribonucleoprotein F
d: Small nuclear ribonucleoprotein G
q: Ubiquitin-like protein 5
X: WW domain-binding protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,762,07162
Polymers2,760,06058
Non-polymers2,0114
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Nuclear cap-binding protein subunit ... , 2 types, 2 molecules A5A1

#1: Protein Nuclear cap-binding protein subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit


Mass: 91960.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q09161
#10: Protein Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa ...20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1


Mass: 18028.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: P52298

+
U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules A2V9CHJA3

#2: 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) / Cell line: Hela / References: UniProt: Q9UK45
#14: 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) / Cell line: Hela / References: UniProt: Q9Y333
#15: 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) / Cell line: Hela / References: UniProt: P62310
#16: 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) / Cell line: Hela / References: UniProt: Q9Y4Z0
#17: 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) / Cell line: Hela / References: UniProt: Q9Y4Y9
#18: 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) / Cell line: Hela / References: UniProt: P62312
#20: 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) / Cell line: Hela / References: UniProt: O95777

+
Splicing factor 3B subunit ... , 6 types, 6 molecules zuTEwx

#3: 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) / Cell line: Hela / References: UniProt: Q9Y3B4
#31: 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) / Cell line: Hela / References: UniProt: O75533
#32: 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) / Cell line: Hela / References: UniProt: Q13435
#33: Protein Splicing factor 3B subunit 3 / Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein ...Pre-mRNA-splicing factor SF3b 130 kDa subunit / SF3b130 / STAF130 / Spliceosome-associated protein 130 / SAP 130


Mass: 135718.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q15393
#34: 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) / Cell line: Hela / References: UniProt: Q15427
#35: 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) / Cell line: Hela / References: UniProt: Q9BWJ5

+
Splicing factor 3A subunit ... , 3 types, 3 molecules Fp4

#4: 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) / Cell line: Hela / References: UniProt: Q15428
#28: 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) / Cell line: Hela / References: UniProt: Q15459
#29: 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) / Cell line: Hela / References: UniProt: Q12874

+
U5 small nuclear ribonucleoprotein ... , 2 types, 2 molecules Ds

#5: 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) / Cell line: Hela / References: UniProt: Q96DI7
#8: 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) / Cell line: Hela / References: UniProt: O75643, RNA helicase

+
U2 small nuclear ribonucleoprotein ... , 2 types, 2 molecules WB

#6: 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) / Cell line: Hela / References: UniProt: P09661
#7: 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) / Cell line: Hela / References: UniProt: P08579

+
Protein , 17 types, 18 molecules QLRKyGAA4v0NrYA6mfqX

#9: 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) / Cell line: Hela / References: UniProt: P41223
#12: 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) / Cell line: Hela / References: UniProt: Q99459
#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) / Cell line: Hela / References: UniProt: Q9P013
#21: Protein Microfibrillar-associated protein 1


Mass: 52050.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: P55081
#22: 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) / Cell line: Hela / References: UniProt: Q7RTV0
#23: Protein Pleiotropic regulator 1


Mass: 57280.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: O43660
#25: 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) / Cell line: Hela / References: UniProt: Q6P2Q9
#30: 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) / Cell line: Hela / References: UniProt: O14776
#36: 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) / Cell line: Hela / References: UniProt: Q13573
#37: Protein Smad nuclear-interacting protein 1 / FHA domain-containing protein SNIP1


Mass: 45880.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q8TAD8
#38: 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) / Cell line: Hela / References: UniProt: Q96NC0
#39: 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) / Cell line: Hela / References: UniProt: Q15029
#40: Protein Serine/arginine repetitive matrix protein 1 / SR-related nuclear matrix protein of 160 kDa / SRm160 / Ser/Arg-related nuclear matrix protein


Mass: 102600.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q8IYB3
#42: 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) / Cell line: Hela / References: UniProt: Q07955
#45: Protein Small nuclear ribonucleoprotein-associated proteins B and B' / snRNP-B / Sm protein B/B' / SmB/B'


Mass: 24642.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: P14678
#50: 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
#51: 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) / Cell line: Hela / References: UniProt: Q9Y2W2

+
RNA chain , 4 types, 4 molecules 52Z6

#11: RNA chain U5 snRNA


Mass: 36908.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: GenBank: 36515
#19: RNA chain U2 snRNA


Mass: 60186.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: GenBank: 36516
#24: RNA chain MINX M3 pre-mRNA


Mass: 73712.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#41: RNA chain U6 snRNA


Mass: 34098.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela

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

#26: 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) / Cell line: Hela / References: UniProt: Q8NAV1
#27: Protein Pre-mRNA-splicing factor RBM22 / RNA-binding motif protein 22 / Zinc finger CCCH domain-containing protein 16


Mass: 46959.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: Q9NW64

+
Small nuclear ribonucleoprotein ... , 6 types, 12 molecules haiblekdjcng

#43: 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) / Cell line: Hela / References: UniProt: P62316
#44: 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) / Cell line: Hela / References: UniProt: P62306
#46: 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) / Cell line: Hlea / References: UniProt: P62318
#47: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


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


Mass: 10817.601 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: UniProt: P62304
#49: 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) / Cell line: Hela / References: UniProt: P62314

+
Non-polymers , 4 types, 4 molecules

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


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


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#55: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3

+
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1pre-Bact-1 spliceosomal complexCOMPLEX#1-#510MULTIPLE SOURCES
2pre-Bact-1 spliceosomal complexCOMPLEX#1-#511MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 1 sec. / Electron dose: 2.25 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84539 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more