9ESH | pdb_00009esh

Structure of a B-state intermediate committed to discard (Bd-I state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of aberrant spliceosome intermediates on their way to disassembly.

Soni, K.Horvath, A.Dybkov, O.Schwan, M.Trakansuebkul, S.Flemming, D.Wild, K.Urlaub, H.Fischer, T.Sinning, I.

(2025) Nat Struct Mol Biol 32: 914-925

  • DOI: https://doi.org/10.1038/s41594-024-01480-7
  • Primary Citation of Related Structures:  
    9ESH, 9ESI

  • PubMed Abstract: 

    Intron removal during pre-mRNA splicing is of extraordinary complexity and its disruption causes a vast number of genetic diseases in humans. While key steps of the canonical spliceosome cycle have been revealed by combined structure-function analyses, structural information on an aberrant spliceosome committed to premature disassembly is not available. Here, we report two cryo-electron microscopy structures of post-B act spliceosome intermediates from Schizosaccharomyces pombe primed for disassembly. We identify the DEAH-box helicase-G-patch protein pair (Gih35-Gpl1, homologous to human DHX35-GPATCH1) and show how it maintains catalytic dormancy. In both structures, Gpl1 recognizes a remodeled active site introduced by an overstabilization of the U5 loop I interaction with the 5' exon leading to a single-nucleotide insertion at the 5' splice site. Remodeling is communicated to the spliceosome surface and the Ntr1 complex that mediates disassembly is recruited. Our data pave the way for a targeted analysis of splicing quality control.


  • Organizational Affiliation
    • Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany. komal.soni@uni-bayreuth.de.

Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor spp42E [auth A]2,363Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf10F [auth B]984Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94316 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf17G [auth C]340Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3H [auth D]97Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BI [auth E]147Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1J [auth F]117Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2K [auth G]115Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EL [auth H]84Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FM [auth I]78Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GN [auth J]77Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor prp5O [auth K]473Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45P [auth L]557Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf5Q [auth M]354Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf11R [auth N]1,284Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf14S [auth O]146Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf2T [auth P]388Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf15U [auth Q]265Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P78794 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf4V [auth R]674Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P87312 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19W [auth S],
X [auth T],
Y [auth U],
Z [auth V]
488Schizosaccharomyces pombeMutation(s): 0 
EC: 2.3.2.27
UniProt
Find proteins for O14011 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cdc5AA [auth W]757Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for P39964 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf3BA [auth X]790Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9P7R9 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor syf2CA [auth Y]229Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf7DA [auth Z]187Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9USV3 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 17EA [auth a]558Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf21FA [auth b]293Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor cwf22GA [auth c]887Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase ppi1HA [auth d]155Schizosaccharomyces pombeMutation(s): 0 
EC: 5.2.1.8
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
UNK1IA [auth f]22Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
G-patch domain-containing protein C1486.03JA [auth m]797Schizosaccharomyces pombeMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
UNK2KA [auth r]346Schizosaccharomyces pombeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein C20H4.06cLA [auth y]534Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for Q9HE07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Putative pre-mRNA-splicing factor ATP-dependent RNA helicase C20H4.09MA [auth z]647Schizosaccharomyces pombeMutation(s): 0 
EC: 3.6.4.13
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
pre-mRNAA [auth 1]29Schizosaccharomyces pombe
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Entity ID: 2
MoleculeChains LengthOrganismImage
U2snRNAB [auth 2]186Schizosaccharomyces pombe
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Entity ID: 3
MoleculeChains LengthOrganismImage
U5snRNAC [auth 5]120Schizosaccharomyces pombe
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Entity ID: 4
MoleculeChains LengthOrganismImage
U6snRNAD [auth 6]99Schizosaccharomyces pombe
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP (Subject of Investigation/LOI)
Query on IHP

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RA [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GTP (Subject of Investigation/LOI)
Query on GTP

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SA [auth B]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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UA [auth M]
VA [auth M]
WA [auth O]
XA [auth O]
YA [auth O]
UA [auth M],
VA [auth M],
WA [auth O],
XA [auth O],
YA [auth O],
ZA [auth P]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

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PA [auth 6]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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NA [auth 6],
OA [auth 6],
QA [auth 6],
TA [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySI 586/6-1
German Research Foundation (DFG)GermanyProject-ID 439669440, TP B03

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection, Database references