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- PDB-5gm6: Cryo-EM structure of the activated spliceosome (Bact complex) at ... -

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Entry
Database: PDB / ID: 5gm6
TitleCryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution
Components
  • (Pre-mRNA-processing factor ...) x 2
  • (Pre-mRNA-splicing factor ...) x 20
  • (Pre-mRNAPrimary transcript) x 2
  • (Saccharomyces cerevisiae strain ...) x 2
  • (Small nuclear ribonucleoprotein ...SnRNP) x 6
  • (U2 snRNP component ...) x 2
  • Cold sensitive U2 snRNA suppressor 1
  • Peptidyl-prolyl isomerase CWC27
  • Pre-mRNA leakage protein 1
  • Pre-mRNA-processing protein 45
  • Pre-mRNA-splicing helicase BRR2
  • Protein HSH49
  • RDS3 complex subunit 10
  • Small nuclear ribonucleoprotein-associated protein B
  • U2 snRNAU2 spliceosomal RNA
KeywordsRNA BINDING PROTEIN/RNA / spliceosome / RNA splicing / Bact / Catalytically activated / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of RNA location / RES complex / response to xenobiotic stimulus / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / snoRNA splicing / cellular bud site selection / cis assembly of pre-catalytic spliceosome / post-mRNA release spliceosomal complex / ATPase, acting on RNA ...maintenance of RNA location / RES complex / response to xenobiotic stimulus / mRNA branch site recognition / U2-type post-mRNA release spliceosomal complex / snoRNA splicing / cellular bud site selection / cis assembly of pre-catalytic spliceosome / post-mRNA release spliceosomal complex / ATPase, acting on RNA / generation of catalytic spliceosome for first transesterification step / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / splicing factor binding / U2-type spliceosomal complex / U2-type catalytic step 1 spliceosome / pICln-Sm protein complex / U4 snRNP / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / SMN-Sm protein complex / pre-mRNA binding / U2 snRNP / commitment complex / mRNA cis splicing, via spliceosome / U2-type catalytic step 2 spliceosome / Prp19 complex / U12-type spliceosomal complex / poly(A) binding / Cul4-RING E3 ubiquitin ligase complex / generation of catalytic spliceosome for second transesterification step / spliceosomal complex assembly / U2-type prespliceosome / spliceosomal snRNP assembly / sno(s)RNA-containing ribonucleoprotein complex / U1 snRNP / mRNA 3'-splice site recognition / precatalytic spliceosome / mRNA 5'-splice site recognition / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / DNA replication origin binding / U5 snRNP / DNA replication initiation / U5 snRNA binding / poly(U) RNA binding / U2 snRNA binding / U6 snRNA binding / pre-mRNA intronic binding / U4/U6 x U5 tri-snRNP complex / U1 snRNA binding / isopeptidase activity / nuclear periphery / catalytic step 2 spliceosome / positive regulation of cell cycle / mRNA export from nucleus / protein peptidyl-prolyl isomerization / spliceosomal complex / positive regulation of RNA splicing / mRNA 3'-UTR binding / RNA splicing / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / RING-type E3 ubiquitin transferase / chromatin / metallopeptidase activity / mRNA splicing, via spliceosome / ubiquitin protein ligase activity / ubiquitin-protein transferase activity / mRNA processing / ribonucleoprotein complex / RNA helicase / RNA helicase activity / cell cycle / GTPase activity / mRNA binding / DNA repair / GTP binding / chromatin binding / mitochondrion / RNA binding / DNA binding / zinc ion binding / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Prp19/Pso4-like / Cyclophilin-like domain superfamily / RNA recognition motif, spliceosomal PrP8 / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / PRP8 domain IV core / Small nuclear ribonucleoprotein E / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 ...Prp19/Pso4-like / Cyclophilin-like domain superfamily / RNA recognition motif, spliceosomal PrP8 / WD40 repeat, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / PRP8 domain IV core / Small nuclear ribonucleoprotein E / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Small nuclear ribonucleoprotein Sm D2 / P-loop containing nucleoside triphosphate hydrolase / Pre-mRNA-processing-splicing factor 8 / SF3A2 domain / Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding / 116kDa U5 small nuclear ribonucleoprotein component, N-terminal / Torus domain / Pre-mRNA-processing factor 17 / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D3 / Small nuclear ribonucleoprotein F / SF3B4, RNA recognition motif 1 / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / Slt11, RNA recognition motif / EF-G domain III/V-like / 116kDa U5 small nuclear ribonucleoprotein component, C-terminal / C2 domain superfamily / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Zinc finger C2H2 superfamily / Zinc finger, RING/FYVE/PHD-type / LSM domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / DEAD/DEAH box helicase domain / Domain of unknown function DUF1605 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Ribonuclease H-like superfamily / PRO8NT domain / PROCN domain / Nucleotide-binding alpha-beta plait domain superfamily / PROCT domain / Tetratricopeptide repeat-containing domain / mRNA splicing factor Cwf21 domain / Bud13 / mRNA splicing factor SYF2 / Pre-mRNA-splicing factor 19 / Helicase superfamily 1/2, ATP-binding domain / Ribosomal protein S5 domain 2-type fold, subgroup / WD40/YVTN repeat-like-containing domain superfamily / MIF4G-like domain superfamily / Armadillo-type fold / Sm-like protein Lsm6/SmF / SKI-interacting protein, SKIP / Myb domain / WD40-repeat-containing domain / BUD31/G10-related, conserved site / RNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Homeobox-like domain superfamily / FHA domain / Domain of unknown function (DUF382) / PSP / Zinc-finger of C2H2 type / Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) / PHF5-like protein / Splicing factor 3B subunit 10 (SF3b10) / WD domain, G-beta repeat / SKIP/SNW domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / Torus domain / Cwf15/Cwc15 cell cycle control protein / G10 protein / Pre-mRNA-splicing factor of RES complex / CPSF A subunit region / cwf21 domain / Helicase associated domain (HA2) / Oligonucleotide/oligosaccharide-binding (OB)-fold / MA3 domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, C3HC4 type (RING finger) / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Myb-like DNA-binding domain / pre-mRNA splicing factor component / HAT (Half-A-TPR) repeat / SYF2 splicing factor / LSM domain / Mono-functional DNA-alkylating methyl methanesulfonate N-term / 116 kDa U5 small nuclear ribonucleoprotein component N-terminus / Winged helix DNA-binding domain superfamily / PRO8NT (NUC069), PrP8 N-terminal domain / Zinc finger, CCCH-type superfamily / MPN domain / Splicing factor 3B subunit 1-like / Pre-mRNA-processing factor 19 / Pre-mRNA-splicing factor Cwc2/Slt11 / Pre-mRNA-splicing factor Cwc2 / Pre-mRNA-splicing factor CWC24-like / Brr2, N-terminal helicase PWI domain / Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily
Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor SLT11 / Pre-mRNA-splicing factor 8 / Pre-mRNA-processing factor 19 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing factor BUD31 / Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / RDS3 complex subunit 10 ...Small nuclear ribonucleoprotein-associated protein B / Small nuclear ribonucleoprotein G / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor SLT11 / Pre-mRNA-splicing factor 8 / Pre-mRNA-processing factor 19 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing factor BUD31 / Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / RDS3 complex subunit 10 / Pre-mRNA-splicing factor SNU114 / Pre-mRNA-processing factor 17 / U2 snRNP component IST3 / Pre-mRNA-splicing factor CWC2 / Peptidyl-prolyl isomerase CWC27 / Pre-mRNA-splicing factor CWC21 / Pre-mRNA-splicing factor CEF1 / Pre-mRNA-splicing factor CWC15 / Pre-mRNA-splicing factor SYF1 / Pre-mRNA-splicing factor RSE1 / Pre-mRNA-splicing factor SNT309 / Small nuclear ribonucleoprotein Sm D2 / Pre-mRNA-splicing factor RDS3 / Pre-mRNA-splicing factor PRP11 / Pre-mRNA leakage protein 1 / Pre-mRNA-splicing factor CLF1 / Cold sensitive U2 snRNA suppressor 1 / Small nuclear ribonucleoprotein E / Pre-mRNA-splicing factor PRP46 / Protein HSH49 / gb:1039023403: / gb:1039022925: / Small nuclear ribonucleoprotein F / Pre-mRNA-splicing factor CWC24 / Pre-mRNA-splicing factor CWC22 / Pre-mRNA-splicing factor SYF2 / U2 snRNP component HSH155 / Pre-mRNA-splicing factor CWC26 / Small nuclear ribonucleoprotein Sm D3 / Pre-mRNA-splicing helicase BRR2
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYan, C. / Wan, R. / Bai, R. / Huang, G. / Shi, Y.
CitationJournal: Science / Year: 2016
Title: Structure of a yeast activated spliceosome at 3.5 Å resolution.
Authors: Chuangye Yan / Ruixue Wan / Rui Bai / Gaoxingyu Huang / Yigong Shi /
Abstract: Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome ...Pre-messenger RNA (pre-mRNA) splicing is carried out by the spliceosome, which undergoes an intricate assembly and activation process. Here, we report an atomic structure of an activated spliceosome (known as the B(act) complex) from Saccharomyces cerevisiae, determined by cryo-electron microscopy at an average resolution of 3.52 angstroms. The final refined model contains U2 and U5 small nuclear ribonucleoprotein particles (snRNPs), U6 small nuclear RNA (snRNA), nineteen complex (NTC), NTC-related (NTR) protein, and a 71-nucleotide pre-mRNA molecule, which amount to 13,505 amino acids from 38 proteins and a combined molecular mass of about 1.6 megadaltons. The 5' exon is anchored by loop I of U5 snRNA, whereas the 5' splice site (5'SS) and the branch-point sequence (BPS) of the intron are specifically recognized by U6 and U2 snRNA, respectively. Except for coordination of the catalytic metal ions, the RNA elements at the catalytic cavity of Prp8 are mostly primed for catalysis. The catalytic latency is maintained by the SF3b complex, which encircles the BPS, and the splicing factors Cwc24 and Prp11, which shield the 5' exon-5'SS junction. This structure, together with those determined earlier, outlines a molecular framework for the pre-mRNA splicing reaction.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Other
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor 8
B: Pre-mRNA-splicing helicase BRR2
C: Pre-mRNA-splicing factor SNU114
D: Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequence
E: Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence
F: Pre-mRNA-splicing factor RSE1
H: Cold sensitive U2 snRNA suppressor 1
I: Pre-mRNA-splicing factor PRP11
J: Pre-mRNA-splicing factor RDS3
K: RDS3 complex subunit 10
L: U2 snRNA
N: Pre-mRNA
M: Pre-mRNA
O: Pre-mRNA-splicing factor PRP46
P: Pre-mRNA-processing protein 45
Q: Pre-mRNA-splicing factor SLT11
R: Pre-mRNA-splicing factor CWC2
S: Pre-mRNA-splicing factor CWC15
T: Pre-mRNA-splicing factor BUD31
U: Pre-mRNA leakage protein 1
V: U2 snRNP component IST3
W: Pre-mRNA-splicing factor CWC26
Y: Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2
Z: Pre-mRNA-splicing factor CWC22
a: Pre-mRNA-splicing factor CWC24
b: Peptidyl-prolyl isomerase CWC27
c: Pre-mRNA-splicing factor CEF1
G: U2 snRNP component HSH155
d: Pre-mRNA-splicing factor CLF1
X: Pre-mRNA-splicing factor CWC21
v: Pre-mRNA-splicing factor SYF1
e: Protein HSH49
f: Pre-mRNA-splicing factor SYF2
o: Pre-mRNA-processing factor 19
p: Pre-mRNA-processing factor 19
q: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
t: Pre-mRNA-splicing factor SNT309
n: Pre-mRNA-processing factor 17
k: Small nuclear ribonucleoprotein-associated protein B
i: Small nuclear ribonucleoprotein E
h: Small nuclear ribonucleoprotein F
j: Small nuclear ribonucleoprotein G
l: Small nuclear ribonucleoprotein Sm D3
m: Small nuclear ribonucleoprotein Sm D1
g: Small nuclear ribonucleoprotein Sm D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,679,38966
Polymers2,677,46746
Non-polymers1,92220
Water0
1


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

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Components

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Pre-mRNA-splicing factor ... , 20 types, 20 molecules ACFIJOQRSTWYZacdXvft

#1: Protein Pre-mRNA-splicing factor 8


Mass: 265949.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P33334
#3: Protein Pre-mRNA-splicing factor SNU114 / 114 kDa U5 small nuclear ribonucleoprotein component / Growth inhibitory protein 10


Mass: 114174.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P36048
#6: Protein Pre-mRNA-splicing factor RSE1 / RNA splicing and ER to Golgi transport factor 1 / Spliceosome-associated protein 130


Mass: 153956.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04693
#8: Protein Pre-mRNA-splicing factor PRP11


Mass: 29962.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07350
#9: Protein Pre-mRNA-splicing factor RDS3 / Regulator of drug sensitivity 3


Mass: 12283.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06835
#14: Protein Pre-mRNA-splicing factor PRP46 / Complexed with CEF1 protein 1 / PRP nineteen-associated complex protein 50


Mass: 50771.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12417
#16: Protein Pre-mRNA-splicing factor SLT11 / Extracellular mutant protein 2 / Synthetic lethality with U2 protein 11


Mass: 40988.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38241
#17: Protein Pre-mRNA-splicing factor CWC2 / Complexed with CEF1 protein 2 / PRP19-associated complex protein 40


Mass: 38486.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12046
#18: Protein Pre-mRNA-splicing factor CWC15 / Complexed with CEF1 protein 15


Mass: 19975.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03772
#19: Protein Pre-mRNA-splicing factor BUD31 / Bud site selection protein 31 / Complexed with CEF1 protein 14


Mass: 18484.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P25337
#22: Protein Pre-mRNA-splicing factor CWC26 / Bud site selection protein 13 / Complexed with CEF1 protein 26


Mass: 30529.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P46947
#23: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 / Pre-mRNA-processing protein 2


Mass: 99947.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20095, RNA helicase
#24: Protein Pre-mRNA-splicing factor CWC22 / Complexed with CEF1 protein 22


Mass: 67386.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53333
#25: Protein Pre-mRNA-splicing factor CWC24 / Complexed with CEF1 protein 24


Mass: 29797.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53769
#27: Protein Pre-mRNA-splicing factor CEF1 / PRP nineteen-associated complex protein 85


Mass: 61057.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (natural) Saccharomyces cerevisiae S288c (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03654
#29: Protein Pre-mRNA-splicing factor CLF1 / Crooked neck-like factor 1 / PRP19-associated complex protein 77


Mass: 68044.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (natural) Saccharomyces cerevisiae S288c (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12309
#30: Protein Pre-mRNA-splicing factor CWC21 / Complexed with CEF1 protein 21


Mass: 15793.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03375
#31: Protein Pre-mRNA-splicing factor SYF1 / PRP19-associated complex protein 90s / Synthetic lethal with CDC40 protein 1


Mass: 78125.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae S288c (yeast), (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04048
#33: Protein Pre-mRNA-splicing factor SYF2 / PRP19 complex protein 31 / Synthetic lethal with CDC40 protein 2


Mass: 24850.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53277
#35: Protein Pre-mRNA-splicing factor SNT309 / PRP19-associated complex protein 25 / Synergistic to PRP19 mutation protein 309


Mass: 20741.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06091

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Protein , 8 types, 8 molecules BHKPUbek

#2: Protein Pre-mRNA-splicing helicase BRR2 / Protein Snu246


Mass: 246470.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32639, RNA helicase
#7: Protein Cold sensitive U2 snRNA suppressor 1


Mass: 50339.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02554
#10: Protein RDS3 complex subunit 10 / Splicing factor 3b subunit


Mass: 10045.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P0C074
#15: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P28004
#20: Protein Pre-mRNA leakage protein 1


Mass: 24100.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q07930
#26: Protein Peptidyl-prolyl isomerase CWC27 / PPIase CWC27 / Complexed with CEF1 protein 27 / Rotamase CWC27


Mass: 35080.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02770, peptidylprolyl isomerase
#32: Protein Protein HSH49


Mass: 24534.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q99181
#37: Protein Small nuclear ribonucleoprotein-associated protein B / snRNP-B / Sm protein B / SmB


Mass: 22426.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40018

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Saccharomyces cerevisiae strain ... , 2 types, 2 molecules DE

#4: RNA chain Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequence


Mass: 68643.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039023403
#5: RNA chain Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence


Mass: 35883.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / References: GenBank: 1039022925

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RNA chain , 3 types, 3 molecules LNM

#11: RNA chain U2 snRNA / U2 spliceosomal RNA


Mass: 376267.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#12: RNA chain Pre-mRNA / Primary transcript


Mass: 7864.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)
#13: RNA chain Pre-mRNA / Primary transcript


Mass: 18915.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast)

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U2 snRNP component ... , 2 types, 2 molecules VG

#21: Protein U2 snRNP component IST3 / Increased sodium tolerance protein 3 / U2 snRNP protein SNU17


Mass: 17121.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40565
#28: Protein U2 snRNP component HSH155


Mass: 110166.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P49955

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Pre-mRNA-processing factor ... , 2 types, 5 molecules opqrn

#34: 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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P32523, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#36: Protein Pre-mRNA-processing factor 17 / Cell division control protein 40


Mass: 52128.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40968

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Small nuclear ribonucleoprotein ... , 6 types, 6 molecules ihjlmg

#38: Protein Small nuclear ribonucleoprotein E / snRNP-E / Sm protein E / SmE


Mass: 10385.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12330
#39: Protein Small nuclear ribonucleoprotein F / snRNP-F / Sm protein F / SmF


Mass: 9669.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P54999
#40: Protein Small nuclear ribonucleoprotein G / snRNP-G / Sm protein G / SmG


Mass: 8490.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40204
#41: Protein Small nuclear ribonucleoprotein Sm D3 / Sm-D3 / snRNP core protein D3


Mass: 11240.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P43321
#42: Protein Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / snRNP core protein D1


Mass: 16296.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02260
#43: Protein Small nuclear ribonucleoprotein Sm D2 / Sm-D2 / snRNP core protein D2


Mass: 11021.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q06217

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Non-polymers , 4 types, 20 molecules

#44: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#46: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#47: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Sequence detailsEACH SEQUENCE OF THE c(LOWER-CASE)/d(LOWER-CASE)/v(LOWER-CASE) CHAINS CORRESPONDS TO EACH UNP ...EACH SEQUENCE OF THE c(LOWER-CASE)/d(LOWER-CASE)/v(LOWER-CASE) CHAINS CORRESPONDS TO EACH UNP DATABASE SEQUENCE. CHAIN c(LOWER-CASE) UNP Q03654, CHAIN d(LOWER-CASE) UNP Q12309, CHAIN v(LOWER-CASE) UNP Q04048, BUT THERE ARE UNK RESIDUES(UNKNOWN RESIDUES) IN THE CHAINS. THE AUTHORS DO NOT KNOW HOW THE COORDINATES OF UNK RESIDUES ALIGN WITH THE SEQUENCE. THEREFORE THE RESIDUE NUMBERS IN THE COORDINATES ARE MEANINGLESS. AUTHORS STATE THAT THE CHAIN M IS A PRE-MRNA. THE CHAIN M HAS FIVE UNCLEAR NUCLEOTIDES 'N".

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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: Bact spliceosomal complex / Type: COMPLEX / Entity ID: #1-#43 / Source: NATURAL
Molecular weightValue: 2.0 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 8
Details: CEB buffer (10 mM Tris-HCl, pH 8.0, 75 mM NaCl, 1 mM Mg(OAc)2, 1 mM imidazole, 0.01% NP40, 1 mM TCEP, 0.5 mM EGTA)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 4.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansScanner model: OTHER

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77312 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.5 Å

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