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- PDB-9l5t: Cryo-EM structure of the thermophile spliceosome (state B*Q2) -

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Basic information

Entry
Database: PDB / ID: 9l5t
TitleCryo-EM structure of the thermophile spliceosome (state B*Q2)
Components
  • (Pre-mRNA-processing ...) x 2
  • (Pre-mRNA-splicing factor ...) x 3
  • (Putative pre-mRNA splicing ...) x 7
  • (RNA helicase) x 2
  • (Small nuclear ribonucleoprotein ...) x 4
  • Anaphase-promoting complex subunit 4-like WD40 domain-containing protein
  • CCDC12
  • Delta(14)-sterol reductase
  • GCFC2
  • GPATCH1
  • Nineteen complex-related protein 2-domain-containing protein
  • PRP17
  • PRP8
  • Peptidyl-prolyl cis-trans isomerase
  • Pre-mRNA-splicing factor
  • Putative bud site selection protein
  • SDE2
  • SNU114
  • Sm protein B
  • Sm protein F
  • Suppressor of forked domain-containing protein
  • TFIP11
  • U2 snRNA
  • U5 snRNA
  • U6 snRNA
  • Unknown mRNA
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 / ergosterol biosynthetic process / spliceosomal snRNP complex / 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 / ergosterol biosynthetic process / spliceosomal snRNP complex / 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 / small nuclear ribonucleoprotein complex / spliceosomal tri-snRNP complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type catalytic step 2 spliceosome / U2 snRNP / U1 snRNP / U4 snRNP / U2-type prespliceosome / precatalytic spliceosome / spliceosomal complex assembly / Prp19 complex / protein K63-linked ubiquitination / U5 snRNP / 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 / RNA helicase activity / hydrolase activity / RNA helicase / DNA repair / mRNA binding / endoplasmic reticulum membrane / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Sde2, N-terminal ubiquitin domain / Yeast Splicing regulator sde2, N-terminal ubiquitin domain / Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2. / mRNA splicing factor Cwf18-like / : / : ...Sde2, N-terminal ubiquitin domain / Yeast Splicing regulator sde2, N-terminal ubiquitin domain / Sterol biosynthesis ERG24/DHCR-like / Sterol reductase, conserved site / Ergosterol biosynthesis ERG4/ERG24 family / Sterol reductase family signature 1. / Sterol reductase family signature 2. / mRNA splicing factor Cwf18-like / : / : / cwf18 pre-mRNA splicing factor / Nineteen complex-related protein 2 / Splicing regulator SDE2, SDE2 domain / DHX15, DEXH-box helicase domain / PRP39 C-terminal HAT repeat / cwf21 / Slt11, RNA recognition motif / Pre-mRNA-splicing factor Cwc2, RNA recognition motif / : / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / 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 / : / : / mRNA splicing factor Cwf21 domain / cwf21 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 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / DNA2/NAM7-like helicase / : / MIF4G domain / Myb-like DNA-binding domain / Anaphase-promoting complex subunit 4, WD40 domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Small nuclear ribonucleoprotein D1 / Anaphase-promoting complex subunit 4 WD40 domain / U-box domain profile. / Zinc finger, CCCH-type superfamily / Modified RING finger domain / U-box domain / 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 / Helicase associated domain (HA2), winged-helix / Small nuclear ribonucleoprotein Sm D2 / Small nuclear ribonucleoprotein E / Helicase-associated domain / Small nuclear ribonucleoprotein G / Helicase associated domain (HA2) Add an annotation
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Chem-M7M / : / RNA / RNA (> 10) / RNA (> 100) / Sm protein F / RNA helicase / Putative pre-mRNA splicing protein / RNA helicase ...GUANOSINE-5'-TRIPHOSPHATE / Chem-M7M / : / RNA / RNA (> 10) / RNA (> 100) / Sm protein F / RNA helicase / Putative pre-mRNA splicing protein / RNA helicase / Uncharacterized protein / Small nuclear ribonucleoprotein Sm D1 / Pre-mRNA-splicing factor PRP46 / Pre-mRNA splicing protein / Peptidyl-prolyl cis-trans isomerase / Uncharacterized protein / Delta(14)-sterol reductase / Putative pre-mRNA splicing protein / Putative bud site selection protein / Pre-mRNA-splicing factor SYF2 / Pre-mRNA-splicing factor CWC22 / Pre-mRNA-splicing factor SYF1 / 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 / 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: 3.5 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
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
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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
Y: Pre-mRNA-splicing factor
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
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
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
1: GPATCH1
z: RNA helicase
V: Putative pre-mRNA splicing protein
Z: Putative pre-mRNA splicing protein
CY: Nineteen complex-related protein 2-domain-containing protein
Ck: GCFC2
Cb: TFIP11
8: Unknown mRNA
Cc: RNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,246,73649
Polymers2,245,39942
Non-polymers1,3387
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 2568

#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
#38: RNA chain Unknown mRNA


Mass: 6293.059 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, 18 molecules ACDEFJYNSWlmp1zCYCbCc

#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
#14: 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
#16: 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
#17: 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
#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
#26: Protein Sm protein F / smF


Mass: 10727.227 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: G0RY82
#27: Protein Delta(14)-sterol reductase / smD2 / C-14 sterol reductase / Sterol C14-reductase


Mass: 66785.492 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: G0S405
#29: Protein Sm protein B / smB/B'


Mass: 21425.543 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: G0SHQ3
#31: Protein GPATCH1


Mass: 75861.016 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)
#32: Protein RNA helicase / DHX35


Mass: 74989.750 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: G0RZD6, RNA helicase
#35: Protein Nineteen complex-related protein 2-domain-containing protein


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
#37: Protein TFIP11


Mass: 33293.949 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)
#39: 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

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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
#18: 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 ... , 7 types, 7 molecules ILM0PVZ

#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
#33: Protein Putative pre-mRNA splicing protein / SRRM2


Mass: 26329.277 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: G0S4I7
#34: Protein Putative pre-mRNA splicing protein / CWC22


Mass: 76518.102 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: G0S5W9

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

#15: 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: 65034.551 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, 4 molecules jkou

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


Mass: 10967.812 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: G0S8J0
#25: Protein Small nuclear ribonucleoprotein G / smG / snRNP-G


Mass: 9259.763 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: G0SI53
#28: Protein Small nuclear ribonucleoprotein Sm D1 / smD1 / snRNP core protein D1


Mass: 13033.093 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: G0RZL0
#30: Protein Small nuclear ribonucleoprotein Sm D3 / smD3 / Sm-D3 / snRNP core protein D3


Mass: 12708.680 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: G0SG70

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Protein/peptide , 1 types, 1 molecules Ck

#36: Protein/peptide GCFC2


Mass: 3592.419 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 , 3 types, 7 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationN

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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 B*Q2 / Type: COMPLEX / Entity ID: #1-#39 / 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16442 / Symmetry type: POINT

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