7B9C

Structure of a minimal SF3B core in complex with spliceostatin A (form I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


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Literature

Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors.

Cretu, C.Gee, P.Liu, X.Agrawal, A.Nguyen, T.V.Ghosh, A.K.Cook, A.Jurica, M.Larsen, N.A.Pena, V.

(2021) Nat Commun 12: 4491-4491

  • DOI: 10.1038/s41467-021-24741-1
  • Primary Citation of Related Structures:  
    7B0I, 7B91, 7B92, 7B9C, 7OMF, 7ONB, 7OPI

  • PubMed Abstract: 
  • Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)-a complex chaperoning the selection of branch and 3' splice sites ...

    Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)-a complex chaperoning the selection of branch and 3' splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept.


    Organizational Affiliation

    Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK. vlad.pena@icr.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3A899Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Sf3b3Kiaa0017SAP130
UniProt & NIH Common Fund Data Resources
Find proteins for Q15393 (Homo sapiens)
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Go to UniProtKB:  Q15393
PHAROS:  Q15393
GTEx:  ENSG00000189091 
Find proteins for Q921M3 (Mus musculus)
Explore Q921M3 
Go to UniProtKB:  Q921M3
IMPC:  MGI:1289341
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15393Q921M3
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5B86Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Find proteins for Q9BWJ5 (Homo sapiens)
Explore Q9BWJ5 
Go to UniProtKB:  Q9BWJ5
PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
Entity Groups  
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UniProt GroupQ9BWJ5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1C852Homo sapiensMutation(s): 0 
Gene Names: SF3B1SAP155
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Find proteins for O75533 (Homo sapiens)
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Go to UniProtKB:  O75533
PHAROS:  O75533
GTEx:  ENSG00000115524 
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UniProt GroupO75533
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AD108Homo sapiensMutation(s): 0 
Gene Names: PHF5A
UniProt & NIH Common Fund Data Resources
Find proteins for Q7RTV0 (Homo sapiens)
Explore Q7RTV0 
Go to UniProtKB:  Q7RTV0
PHAROS:  Q7RTV0
GTEx:  ENSG00000100410 
Entity Groups  
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UniProt GroupQ7RTV0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SJT (Subject of Investigation/LOI)
Query on SJT

Download Ideal Coordinates CCD File 
I [auth D]spliceostatin A (form II)
C28 H45 N O8
KFBJURVXOOMXKK-GSHHMAPISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth D],
F [auth D],
G [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

Download Ideal Coordinates CCD File 
H [auth D]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.573α = 90
b = 111.066β = 90
c = 248.757γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-12-14 
  • Released Date: 2021-08-04 
  • Deposition Author(s): Cretu, C., Pena, V.

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyPE 2079/4-1

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release