9L5R | pdb_00009l5r

Cryo-EM structure of the thermophile spliceosome (state ILS)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into spliceosome fidelity: DHX35-GPATCH1- mediated rejection of aberrant splicing substrates.

Li, Y.Fischer, P.Wang, M.Zhou, Q.Song, A.Yuan, R.Meng, W.Chen, F.X.Luhrmann, R.Lau, B.Hurt, E.Cheng, J.

(2025) Cell Res 35: 296-308

  • DOI: https://doi.org/10.1038/s41422-025-01084-w
  • Primary Citation of Related Structures:  
    9L5R, 9L5S, 9L5T

  • PubMed 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 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* Q , 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* Q , 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.


  • Organizational Affiliation
    • Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PRP8D [auth A]2,463Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2E [auth B]326Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S5N3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
SNU114F [auth C]1,011Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
SDE2G [auth D]325Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 4-like WD40 domain-containing proteinH [auth E]352Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S9U7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CCDC12I [auth F]233Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA splicing proteinJ [auth I]839Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Suppressor of forked domain-containing proteinK [auth J]687Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA splicing protein768Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SPF27M [auth K]231Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19N [auth q],
O [auth t],
P [auth r],
Q [auth s]
480Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 2.3.2.27
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Putative bud site selection proteinR [auth N]148Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase167Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor PRP46496Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cell cycle control protein757Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA splicing proteinV [auth M]395Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA splicing proteinW [auth 0]408Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45X [auth R]578Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PRP17Y [auth W]547Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S2N1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA splicing proteinZ [auth P]260Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S754 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factorAA [auth Y]1,416Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EBA [auth a],
KA [auth j]
98Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Sm protein FCA [auth b],
MA [auth l]
94Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RY82 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Delta(14)-sterol reductaseDA [auth c],
NA [auth m]
592Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0S405 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1EA [auth d],
OA [auth o]
118Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Sm protein BFA [auth e],
PA [auth p]
211Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3GA [auth f],
QA [auth u]
114Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GHA [auth g],
LA [auth k]
82Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0SI53 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein A'IA [auth h]242Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
U2 small nuclear ribonucleoprotein B'-like proteinJA [auth i]201Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Nineteen complex-related protein 2-domain-containing proteinRA [auth CY]510Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
G-patch domain-containing proteinSA [auth Cb]975Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
RNA helicaseTA [auth Cc]764Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for G0RY84 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cyclophilin proteinVA [auth Ci]153Thermochaetoides thermophila DSM 1495Mutation(s): 0 
UniProt
Find proteins for G0RZE2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinWA [auth H]22Thermochaetoides thermophila DSM 1495Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U2 snRNAA [auth 2]193Thermochaetoides thermophila DSM 1495
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNAB [auth 5]116Thermochaetoides thermophila DSM 1495
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Entity ID: 3
MoleculeChains LengthOrganismImage
U6 snRNAC [auth 6]101Thermochaetoides thermophila DSM 1495
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Entity ID: 37
MoleculeChains LengthOrganismImage
Unknown mRNAUA [auth 7]101Thermochaetoides thermophila DSM 1495
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

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AB [auth J]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP
Query on GTP

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ZA [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
M7M
Query on M7M

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XA [auth B]N,N,7-trimethylguanosine 5'-(trihydrogen diphosphate)
C13 H23 N5 O11 P2
DHQQIEJARUGVNZ-WOUKDFQISA-N
ZN
Query on ZN

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BB [auth N]
CB [auth N]
DB [auth N]
EB [auth U]
FB [auth M]
BB [auth N],
CB [auth N],
DB [auth N],
EB [auth U],
FB [auth M],
GB [auth M]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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YA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
X [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references