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- PDB-7b9v: Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18... -

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Basic information

Entry
Database: PDB / ID: 7b9v
TitleYeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound
Components
  • (Pre-mRNA-processing ...) x 2
  • (Pre-mRNA-splicing factor ...) x 12
  • (Small nuclear ribonucleoprotein ...) x 6
  • 5' exon of UBC4 mRNA
  • BJ4_G0027490.mRNA.1.CDS.1
  • BJ4_G0054360.mRNA.1.CDS.1
  • BUD31 isoform 1
  • Branched intron and 3' exon of UBC4 pre-mRNA
  • CDC40 isoform 1
  • CLF1 isoform 1
  • CWC22 isoform 1
  • HLJ1_G0053790.mRNA.1.CDS.1
  • NTC20 isoform 1
  • Pre-mRNA-splicing helicase BRR2
  • SNT309 isoform 1
  • SYF1 isoform 1
  • Small nuclear ribonucleoprotein-associated protein B
  • Splicing factor YJU2
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • Unassigned structure
  • Y55_G0042700.mRNA.1.CDS.1
KeywordsSPLICING / spliceosome / RNA / ribozyme
Function / homology
Function and homology information


second spliceosomal transesterification activity / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / pre-mRNA binding ...second spliceosomal transesterification activity / pre-mRNA 3'-splice site binding / post-mRNA release spliceosomal complex / splicing factor binding / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U4/U6 snRNP / Prp19 complex / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / pre-mRNA binding / U2-type catalytic step 1 spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / poly(U) RNA binding / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / precatalytic spliceosome / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / mRNA 5'-splice site recognition / regulation of RNA splicing / mRNA 3'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / helicase activity / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / metallopeptidase activity / nucleic acid binding / RNA helicase activity / RNA helicase / GTPase activity / mRNA binding / GTP binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / cwf21 ...Prp18 / Pre-mRNA-splicing factor 18 / Prp18 domain / Pre-mRNA-splicing factor SLU7 domain / Pre-mRNA-splicing factor SLU7 / Pre-mRNA splicing Prp18-interacting factor / Pre-mRNA-splicing factor Isy1 / Pre-mRNA-splicing factor Isy1 superfamily / Isy1-like splicing family / cwf21 / Torus domain / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Torus domain / Helix hairpin bin domain superfamily / mRNA splicing factor Cwf21 domain / cwf21 domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / BUD31/G10-related, conserved site / G10 protein signature 1. / G10 protein signature 2. / Pre-mRNA-splicing factor Cwf15/Cwc15 / HAT (Half-A-TPR) repeat / Cwf15/Cwc15 cell cycle control protein / Pre-mRNA-splicing factor Cwc2/Slt11 / G10 protein / : / Pre-mRNA-splicing factor BUD31 / U2A'/phosphoprotein 32 family A, C-terminal / occurring C-terminal to leucine-rich repeats / Leucine-rich repeat / Brr2, N-terminal helicase PWI domain / : / N-terminal helicase PWI domain / Pre-mRNA-splicing helicase BRR2 plug domain / Pre-mRNA-splicing factor Syf1-like / Sec63 Brl domain / Snu114, GTP-binding domain / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein F / Sec63 domain / Sec63 Brl domain / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / : / Sm domain profile. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / LSM domain superfamily / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / PROCT domain / Prp8 RNase domain IV, fingers region / PROCT (NUC072) domain / PRO8NT domain / PROCN domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / RNA recognition motif, spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily / Prp8 RNase domain IV, palm region / PRO8NT (NUC069), PrP8 N-terminal domain / PROCN (NUC071) domain / U6-snRNA interacting domain of PrP8 / U5-snRNA binding site 2 of PrP8 / RNA recognition motif of the spliceosomal PrP8 / PRP8 domain IV core / Pre-mRNA-processing-splicing factor 8 / Elongation factor Tu domain 2 / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Leucine-rich repeat profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / D-chiro inositol hexakisphosphate / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Pre-mRNA-splicing factor CLF1 / : ...GUANOSINE-5'-TRIPHOSPHATE / : / D-chiro inositol hexakisphosphate / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / : / Pre-mRNA-splicing factor CLF1 / : / SNU114 isoform 1 / Pre-mRNA-splicing factor 18 / : / : / Pre-mRNA-splicing factor CWC21 / : / : / Pre-mRNA-splicing factor CWC2 / : / : / U2 small nuclear ribonucleoprotein A' / MSL1 isoform 1 / BUD31 isoform 1 / : / BJ4_G0054360.mRNA.1.CDS.1 / : / Pre-mRNA-splicing factor CWC15 / : / : / Pre-mRNA-splicing factor SLU7 / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 / Pre-mRNA-splicing factor ISY1 / Pre-mRNA-splicing helicase BRR2 / Pre-mRNA-splicing factor 8 / Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / Small nuclear ribonucleoprotein Sm D1 / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWilkinson, M.E. / Fica, S.M. / Galej, W.P. / Nagai, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)SPLICE3D United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Mol Cell / Year: 2021
Title: Structural basis for conformational equilibrium of the catalytic spliceosome.
Authors: Max E Wilkinson / Sebastian M Fica / Wojciech P Galej / Kiyoshi Nagai /
Abstract: The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the ...The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (C) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to C before ATP hydrolysis by Prp16 can destabilize the branching conformation. Biochemical assays suggest that these pre-bound factors prime the C complex for conversion to C by Prp16. A complete model of the Prp19 complex (NTC) reveals how the branching factors Yju2 and Isy1 are recruited by the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain tethered to the NTC in the C complex to promote exon ligation. Our results explain how Prp16 action modulates the dynamic binding of step-specific factors to alternatively stabilize the C or C conformation and establish equilibrium of the catalytic spliceosome.
History
DepositionDec 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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Assembly

Deposited unit
2: U2 snRNA
5: U5 snRNA
6: U6 snRNA
A: Pre-mRNA-splicing factor 8
B: Pre-mRNA-splicing helicase BRR2
C: Pre-mRNA-splicing factor SNU114
D: Splicing factor YJU2
E: 5' exon of UBC4 mRNA
F: Pre-mRNA-splicing factor CWC25
G: Pre-mRNA-splicing factor ISY1
H: CWC22 isoform 1
I: Branched intron and 3' exon of UBC4 pre-mRNA
J: BJ4_G0054360.mRNA.1.CDS.1
K: Pre-mRNA-processing protein 45
L: BUD31 isoform 1
M: Pre-mRNA-splicing factor CWC2
N: Pre-mRNA-splicing factor SLT11
O: Y55_G0042700.mRNA.1.CDS.1
P: Pre-mRNA-splicing factor CWC15
Q: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16
R: Pre-mRNA-splicing factor CWC21
S: CLF1 isoform 1
T: SYF1 isoform 1
W: HLJ1_G0053790.mRNA.1.CDS.1
X: Unassigned structure
Y: BJ4_G0027490.mRNA.1.CDS.1
Z: NTC20 isoform 1
a: Pre-mRNA-splicing factor 18
b: Small nuclear ribonucleoprotein-associated protein B
c: Pre-mRNA-splicing factor SLU7
d: Small nuclear ribonucleoprotein Sm D3
e: Small nuclear ribonucleoprotein E
f: Small nuclear ribonucleoprotein F
g: Small nuclear ribonucleoprotein G
h: Small nuclear ribonucleoprotein Sm D1
j: Small nuclear ribonucleoprotein Sm D2
k: Small nuclear ribonucleoprotein-associated protein B
l: Small nuclear ribonucleoprotein Sm D1
m: Small nuclear ribonucleoprotein Sm D2
n: Small nuclear ribonucleoprotein Sm D3
o: CDC40 isoform 1
p: Small nuclear ribonucleoprotein E
q: Small nuclear ribonucleoprotein F
r: Small nuclear ribonucleoprotein G
s: SNT309 isoform 1
t: Pre-mRNA-processing factor 19
u: Pre-mRNA-processing factor 19
v: Pre-mRNA-processing factor 19
w: Pre-mRNA-processing factor 19
y: Pre-mRNA-splicing factor SYF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,572,42067
Polymers2,570,52850
Non-polymers1,89117
Water00
1


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

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Components

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RNA chain , 5 types, 5 molecules 256EI

#1: RNA chain U2 snRNA


Mass: 376267.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#2: RNA chain U5 snRNA


Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#3: RNA chain U6 snRNA


Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#8: RNA chain 5' exon of UBC4 mRNA


Mass: 15041.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#12: RNA chain Branched intron and 3' exon of UBC4 pre-mRNA


Mass: 30200.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Pre-mRNA-splicing factor ... , 12 types, 12 molecules ACFGMNPQRacy

#4: Protein Pre-mRNA-splicing factor 8 / Prp8


Mass: 279867.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P33334
#6: Protein Pre-mRNA-splicing factor SNU114 / SNU114 isoform 1


Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PW35
#9: Protein Pre-mRNA-splicing factor CWC25


Mass: 20010.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q526
#10: Protein Pre-mRNA-splicing factor ISY1


Mass: 27625.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6V8S636
#16: Protein Pre-mRNA-splicing factor CWC2


Mass: 38486.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q155
#17: Protein Pre-mRNA-splicing factor SLT11


Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0Z2
#19: Protein Pre-mRNA-splicing factor CWC15


Mass: 19975.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0Y8G8
#20: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16


Mass: 121815.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6V8RSY7
#21: Protein Pre-mRNA-splicing factor CWC21


Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZG6
#28: Protein Pre-mRNA-splicing factor 18


Mass: 28414.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PX22
#30: Protein Pre-mRNA-splicing factor SLU7


Mass: 44722.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6V8RGB0
#40: Protein Pre-mRNA-splicing factor SYF2 / Pre-mRNA-splicing factor syf2


Mass: 24850.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PX61

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Protein , 15 types, 16 molecules BDHJLOSTWXYZbkos

#5: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246 / yeast Brr2


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32639, RNA helicase
#7: Protein Splicing factor YJU2


Mass: 33360.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1B9A1
#11: Protein CWC22 isoform 1


Mass: 67386.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1E9
#13: Protein BJ4_G0054360.mRNA.1.CDS.1 / PRP46 isoform 1


Mass: 50771.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q605
#15: Protein BUD31 isoform 1 / EM14S01-3B_G0005920.mRNA.1.CDS.1 / HLJ1_G0006010.mRNA.1.CDS.1 / JXXY16.1_G0005970.mRNA.1.CDS.1 / ...EM14S01-3B_G0005920.mRNA.1.CDS.1 / HLJ1_G0006010.mRNA.1.CDS.1 / JXXY16.1_G0005970.mRNA.1.CDS.1 / Pre-mRNA-splicing factor BUD31 / SX2_G0005960.mRNA.1.CDS.1 / XXYS1_G0005950.mRNA.1.CDS.1 / Y55_G0006020.mRNA.1.CDS.1


Mass: 18484.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q3N1
#18: Protein Y55_G0042700.mRNA.1.CDS.1


Mass: 67085.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0ZW46
#22: Protein CLF1 isoform 1 / Pre-mRNA-splicing factor CLF1


Mass: 82555.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PT67
#23: Protein SYF1 isoform 1


Mass: 100344.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0A4
#24: Protein HLJ1_G0053790.mRNA.1.CDS.1 / LEA1 isoform 1 / Y55_G0053650.mRNA.1.CDS.1


Mass: 27232.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q2G3
#25: Protein Unassigned structure


Mass: 20443.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#26: Protein BJ4_G0027490.mRNA.1.CDS.1 / HN1_G0027200.mRNA.1.CDS.1 / MSL1 isoform 1 / SX2_G0029270.mRNA.1.CDS.1 / Y55_G0027550.mRNA.1.CDS.1


Mass: 12850.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q318
#27: Protein NTC20 isoform 1


Mass: 15992.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1C0
#29: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB / U5 SmB


Mass: 22426.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P40018
#37: Protein CDC40 isoform 1


Mass: 52208.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYD5
#38: Protein SNT309 isoform 1 / Y55_G0056570.mRNA.1.CDS.1


Mass: 20741.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q641

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Pre-mRNA-processing ... , 2 types, 5 molecules Ktuvw

#14: Protein Pre-mRNA-processing protein 45


Mass: 42548.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTY9
#39: Protein
Pre-mRNA-processing factor 19


Mass: 56629.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5PQI0, RING-type E3 ubiquitin transferase

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Small nuclear ribonucleoprotein ... , 6 types, 12 molecules dnepfqgrhljm

#31: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3 / U5 SmD3


Mass: 11240.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P43321
#32: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE / U5 SmE


Mass: 10385.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q12330
#33: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P54999
#34: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: P40204
#35: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1 / U4 SmD1


Mass: 16296.798 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q02260
#36: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2 / SmD2


Mass: 12876.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: BCY123 / References: UniProt: Q06217

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Non-polymers , 5 types, 17 molecules

#41: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#42: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#43: Chemical ChemComp-KGN / D-chiro inositol hexakisphosphate


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#44: 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
#45: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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: Yeast C complex spliceosome with Prp18/Slu7 bound / Type: COMPLEX / Entity ID: #1-#40 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
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
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 9 / Num. of real images: 24115

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
ISOLDE1.0.1model building
UCSF ChimeraX1.0/v9model building
EM software
IDNameVersionCategory
7Coot0.9.4model fitting
12RELION3.13D reconstruction
13PHENIXdev-3965model refinement
14ISOLDE1.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 403474 / Symmetry type: POINT

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