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- PDB-9l5r: Cryo-EM structure of the thermophile spliceosome (state ILS) -

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Entry
Database: PDB / ID: 9l5r
TitleCryo-EM structure of the thermophile spliceosome (state ILS)
Components
  • (Pre-mRNA-processing ...) x 2
  • (Pre-mRNA-splicing factor ...) x 3
  • (Putative pre-mRNA splicing ...) x 5
  • (Small nuclear ribonucleoprotein ...) x 4
  • (U2 small nuclear ribonucleoprotein ...) x 2
  • Anaphase-promoting complex subunit 4-like WD40 domain-containing protein
  • CCDC12
  • Cell cycle control protein
  • Delta(14)-sterol reductase
  • G-patch domain-containing protein
  • Nineteen complex-related protein 2-domain-containing protein
  • PRP17
  • PRP8
  • Peptidyl-prolyl cis-trans isomerase
  • Pre-mRNA-splicing factor
  • Putative bud site selection protein
  • Putative cyclophilin protein
  • RNA helicase
  • SDE2
  • SNU114
  • Sm protein B
  • Sm protein F
  • Suppressor of forked domain-containing protein
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • Unknown mRNA
  • Unknown protein
KeywordsSPLICING/RNA / Spilceosome / DHX15 / DHX35 / GPATCH1 / SPLICING-RNA complex
Function / homology
Function and homology information


Delta14-sterol reductase activity / spliceosomal complex disassembly / U2-type post-mRNA release spliceosomal complex / spliceosomal snRNP complex / ergosterol biosynthetic process / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding ...Delta14-sterol reductase activity / spliceosomal complex disassembly / U2-type post-mRNA release spliceosomal complex / spliceosomal snRNP complex / ergosterol biosynthetic process / post-mRNA release spliceosomal complex / generation of catalytic spliceosome for first transesterification step / pICln-Sm protein complex / U2-type catalytic step 1 spliceosome / pre-mRNA binding / snRNP binding / SMN-Sm protein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / nuclear lumen / U2 snRNP / U1 snRNP / U4 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Prp19 complex / protein K63-linked ubiquitination / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / RNA splicing / peptidylprolyl isomerase / spliceosomal complex / peptidyl-prolyl cis-trans isomerase activity / helicase activity / mRNA splicing, via spliceosome / RING-type E3 ubiquitin transferase / mRNA processing / ubiquitin protein ligase activity / protein folding / regulation of gene expression / nucleic acid binding / RNA helicase activity / hydrolase activity / RNA helicase / ribonucleoprotein complex / DNA repair / mRNA binding / endoplasmic reticulum membrane / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sde2, N-terminal ubiquitin domain / Yeast Splicing regulator sde2, N-terminal ubiquitin domain / Tuftelin interacting protein, N-terminal domain / Tuftelin interacting protein N terminal / Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2. / GCF, C-terminal ...Sde2, N-terminal ubiquitin domain / Yeast Splicing regulator sde2, N-terminal ubiquitin domain / Tuftelin interacting protein, N-terminal domain / Tuftelin interacting protein N terminal / Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2. / GCF, C-terminal / GC-rich sequence DNA-binding factor-like protein / mRNA splicing factor Cwf18-like / : / TFP11/STIP/Ntr1 / : / cwf18 pre-mRNA splicing factor / Nineteen complex-related protein 2 / Splicing regulator SDE2, SDE2 domain / Cwf19-like protein, C-terminal domain-2 / Cwf19-like, C-terminal domain-1 / Cwf19-like protein / Protein similar to CwfJ C-terminus 2 / Protein similar to CwfJ C-terminal / DHX15, DEXH-box helicase domain / PRP39 C-terminal HAT repeat / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / Peptidyl-prolyl cis-trans isomerase E, RNA recognition motif / Pre-mRNA-splicing factor SPF27 / Torus domain / Breast carcinoma amplified sequence 2 (BCAS2) / Torus domain / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / mRNA splicing factor SYF2 / SYF2 splicing factor / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / Pre-mRNA-processing factor 17 / PRP39 N-terminal HAT repeat / : / Pre-mRNA-splicing factor 19 / Pre-mRNA-processing factor 19 / : / Prp19/Pso4-like / : / Pre-mRNA-splicing factor SYF1 middle HAT repeat / Myb-like domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, cyclophilin A-like / BUD31/G10-related, conserved site / G10 protein signature 1. / : / : / STL11, N-terminal / : / Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat / SKI-interacting protein SKIP, SNW domain / SKI-interacting protein, SKIP / SKIP/SNW domain / DNA2/NAM7 helicase, helicase domain / : / AAA domain / Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat / Pre-mRNA-splicing factor Cwf15/Cwc15 / Cwf15/Cwc15 cell cycle control protein / WD repeat Prp46/PLRG1-like / Pre-mRNA-splicing factor Cwc2/Slt11 / : / G10 protein / Pre-mRNA-splicing factor BUD31 / Pre-mRNA splicing factor component Cdc5p/Cef1, C-terminal / : / : / pre-mRNA splicing factor component / DNA2/NAM7-like helicase / : / Myb-like DNA-binding domain / Anaphase-promoting complex subunit 4, WD40 domain / U2 small nuclear ribonucleoprotein A' / Small nuclear ribonucleoprotein D1 / Anaphase-promoting complex subunit 4 WD40 domain / U-box domain profile. / HIT-like superfamily / Zinc finger, CCCH-type superfamily / Modified RING finger domain / U-box domain / Leucine-rich repeat / Pre-mRNA-splicing factor Syf1-like / : / Small nuclear ribonucleoprotein Sm D3 / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Chem-M7M / : / RNA / RNA (> 10) / RNA (> 100) / Sm protein F / RNA helicase / Putative pre-mRNA splicing protein ...GUANOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Chem-M7M / : / RNA / RNA (> 10) / RNA (> 100) / Sm protein F / RNA helicase / Putative pre-mRNA splicing protein / Uncharacterized protein / Putative cyclophilin protein / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor PRP46 / Pre-mRNA splicing protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / G-patch domain-containing protein / Delta(14)-sterol reductase / Putative bud site selection protein / Pre-mRNA-splicing factor SYF2 / Pre-mRNA-splicing factor SYF1 / U2 small nuclear ribonucleoprotein A' / Cell cycle control protein / Putative pre-mRNA splicing protein / Pre-mRNA-splicing factor CWC2 / Putative pre-mRNA splicing protein / Small nuclear ribonucleoprotein E / Anaphase-promoting complex subunit 4-like WD40 domain-containing protein / U2 small nuclear ribonucleoprotein B'-like protein / Uncharacterized protein / Pre-mRNA-splicing factor SPF27 / Pre-mRNA-processing protein 45 / Pre-mRNA-splicing factor / Pre-mRNA-processing factor 19 / Small nuclear ribonucleoprotein Sm D3 / Sm protein B / Small nuclear ribonucleoprotein G / Nineteen complex-related protein 2-domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi, Y. / Fischer, P. / Wang, M. / Yuan, R. / Meng, W. / Luehrmann, R. / Lau, B. / Hurt, E. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2025
Title: Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates.
Authors: Yi Li / Paulina Fischer / Mengjiao Wang / Qianxing Zhou / Aixia Song / Rui Yuan / Wanyu Meng / Fei Xavier Chen / Reinhard Lührmann / Benjamin Lau / Ed Hurt / Jingdong Cheng /
Abstract: The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into the step-wise ...The spliceosome, a highly dynamic macromolecular assembly, catalyzes the precise removal of introns from pre-mRNAs. Recent studies have provided comprehensive structural insights into the step-wise assembly, catalytic splicing and final disassembly of the spliceosome. However, the molecular details of how the spliceosome recognizes and rejects suboptimal splicing substrates remained unclear. Here, we show cryo-electron microscopy structures of spliceosomal quality control complexes from a thermophilic eukaryote, Chaetomium thermophilum. The spliceosomes, henceforth termed B*, are stalled at a catalytically activated state but prior to the first splicing reaction due to an aberrant 5' splice site conformation. This state is recognized by G-patch protein GPATCH1, which is docked onto PRP8-EN and -RH domains and has recruited the cognate DHX35 helicase to its U2 snRNA substrate. In B*, DHX35 has dissociated the U2/branch site helix, while the disassembly helicase DHX15 is docked close to its U6 RNA 3'-end substrate. Our work thus provides mechanistic insights into the concerted action of two spliceosomal helicases in maintaining splicing fidelity by priming spliceosomes that are bound to aberrant splice substrates for disassembly.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: U2 snRNA
5: U5 snRNA
6: U6 snRNA
A: PRP8
B: Pre-mRNA-splicing factor SYF2
C: SNU114
D: SDE2
E: Anaphase-promoting complex subunit 4-like WD40 domain-containing protein
F: CCDC12
I: Putative pre-mRNA splicing protein
J: Suppressor of forked domain-containing protein
L: Putative pre-mRNA splicing protein
K: Pre-mRNA-splicing factor SPF27
q: Pre-mRNA-processing factor 19
t: Pre-mRNA-processing factor 19
r: Pre-mRNA-processing factor 19
s: Pre-mRNA-processing factor 19
N: Putative bud site selection protein
S: Peptidyl-prolyl cis-trans isomerase
T: Pre-mRNA-splicing factor PRP46
U: Cell cycle control protein
M: Putative pre-mRNA splicing protein
0: Putative pre-mRNA splicing protein
R: Pre-mRNA-processing protein 45
W: PRP17
P: Putative pre-mRNA splicing protein
Y: Pre-mRNA-splicing factor
a: Small nuclear ribonucleoprotein E
b: Sm protein F
c: Delta(14)-sterol reductase
d: Small nuclear ribonucleoprotein Sm D1
e: Sm protein B
f: Small nuclear ribonucleoprotein Sm D3
g: Small nuclear ribonucleoprotein G
h: U2 small nuclear ribonucleoprotein A'
i: U2 small nuclear ribonucleoprotein B'-like protein
j: Small nuclear ribonucleoprotein E
k: Small nuclear ribonucleoprotein G
l: Sm protein F
m: Delta(14)-sterol reductase
o: Small nuclear ribonucleoprotein Sm D1
p: Sm protein B
u: Small nuclear ribonucleoprotein Sm D3
CY: Nineteen complex-related protein 2-domain-containing protein
Cb: G-patch domain-containing protein
Cc: RNA helicase
7: Unknown mRNA
Ci: Putative cyclophilin protein
H: Unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,384,31059
Polymers2,382,22349
Non-polymers2,08710
Water00
1


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

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Components

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RNA chain , 4 types, 4 molecules 2567

#1: RNA chain U2 snRNA


Mass: 61393.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
#2: RNA chain U5 snRNA


Mass: 36997.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
#3: RNA chain U6 snRNA


Mass: 32443.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: GenBank: 170940748
#37: RNA chain Unknown mRNA


Mass: 22184.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Protein , 18 types, 21 molecules ACDEFJNSUWYblcmepCYCbCcCi

#4: Protein PRP8


Mass: 285131.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
#6: Protein SNU114


Mass: 113867.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
#7: Protein SDE2 / SDE2


Mass: 35780.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RZD9
#8: Protein Anaphase-promoting complex subunit 4-like WD40 domain-containing protein / U5-40K


Mass: 38229.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S9U7
#9: Protein CCDC12 / CCDC12


Mass: 25360.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SDJ6
#11: Protein Suppressor of forked domain-containing protein / SYF3


Mass: 82195.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S0H7
#15: Protein Putative bud site selection protein / BUD31


Mass: 17176.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S4Q2
#16: Protein Peptidyl-prolyl cis-trans isomerase / PPIL1 / PPIase


Mass: 18361.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S1V3, peptidylprolyl isomerase
#18: Protein Cell cycle control protein / CWF19L2


Mass: 88162.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S730
#22: Protein PRP17 / PRP17


Mass: 61222.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S2N1
#24: Protein Pre-mRNA-splicing factor / AQR


Mass: 161045.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SFN9
#26: Protein Sm protein F / smF


Mass: 10727.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RY82
#27: Protein Delta(14)-sterol reductase / smD2 / C-14 sterol reductase / Sterol C14-reductase


Mass: 66785.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S405
#29: Protein Sm protein B / smB/B'


Mass: 21425.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SHQ3
#34: Protein Nineteen complex-related protein 2-domain-containing protein / GCFC2


Mass: 56472.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SI54
#35: Protein G-patch domain-containing protein / TFIP11


Mass: 110801.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S394
#36: Protein RNA helicase / DHX15


Mass: 87155.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RY84, RNA helicase
#38: Protein Putative cyclophilin protein / PPIE


Mass: 16600.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RZE2

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Pre-mRNA-splicing factor ... , 3 types, 3 molecules BKT

#5: Protein Pre-mRNA-splicing factor SYF2 / SYF2


Mass: 36945.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S5N3
#13: Protein Pre-mRNA-splicing factor SPF27 / SPF27


Mass: 25550.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SDM8
#17: Protein Pre-mRNA-splicing factor PRP46 / PLRG1 / Pre-mRNA-processing protein 46


Mass: 54207.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S066

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Putative pre-mRNA splicing ... , 5 types, 5 molecules ILM0P

#10: Protein Putative pre-mRNA splicing protein / SYF1


Mass: 97944.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S620
#12: Protein Putative pre-mRNA splicing protein / CDC5L


Mass: 86636.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S8A6
#19: Protein Putative pre-mRNA splicing protein / ECM2


Mass: 42241.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RYD8
#20: Protein Putative pre-mRNA splicing protein / CWC2


Mass: 45885.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S7S7
#23: Protein Putative pre-mRNA splicing protein / CWC15


Mass: 28956.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S754

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

#14: Protein
Pre-mRNA-processing factor 19 / PRP19


Mass: 51844.324 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SFY0, RING-type E3 ubiquitin transferase
#21: Protein Pre-mRNA-processing protein 45 / SKIP


Mass: 65194.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SF87

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Small nuclear ribonucleoprotein ... , 4 types, 8 molecules ajdofugk

#25: Protein Small nuclear ribonucleoprotein E / smE / snRNP-E / Sm protein E


Mass: 10967.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S8J0
#28: Protein Small nuclear ribonucleoprotein Sm D1 / smD1


Mass: 13033.093 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RZL0
#30: Protein Small nuclear ribonucleoprotein Sm D3 / smD3 / Sm-D3 / snRNP core protein D3


Mass: 12708.680 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SG70
#31: Protein Small nuclear ribonucleoprotein G / smG / snRNP-G


Mass: 9259.763 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SI53

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

#32: Protein U2 small nuclear ribonucleoprotein A' / U2 snrnp A


Mass: 27249.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0S6F0
#33: Protein U2 small nuclear ribonucleoprotein B'-like protein / U2 snrnp B


Mass: 21744.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SBL9

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Protein/peptide , 1 types, 1 molecules H

#39: Protein/peptide Unknown protein


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)

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Non-polymers , 5 types, 10 molecules

#40: Chemical ChemComp-M7M / N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)


Mass: 487.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H23N5O11P2
#41: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#42: 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
#43: 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
#44: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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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: spliceosome in state ILS / Type: COMPLEX / Entity ID: #1-#36, #38 / Source: NATURAL
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
4RELIONCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
CTF correctionDetails: Relion / Type: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77668 / Symmetry type: POINT

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