5ZYA

SF3b spliceosomal complex bound to E7107


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 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

The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action

Finci, L.I.Zhang, X.Huang, X.Zhou, Q.Tsai, J.Teng, T.Agrawal, A.Chan, B.Irwin, S.Karr, C.Cook, A.Zhu, P.Reynolds, D.Smith, P.G.Fekkes, P.Buonamici, S.Larsen, N.A.

(2018) Genes Dev. 32: 309-320

  • DOI: 10.1101/gad.311043.117
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RN ...

    Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1 R1074H and PHF5A Y36C The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure-activity relationship (SAR) on the PHF5A R38C mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.


    Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 5
B
86Homo sapiensMutation(s): 0 
Gene Names: SF3B5 (SF3B10)
Find proteins for Q9BWJ5 (Homo sapiens)
Go to Gene View: SF3B5
Go to UniProtKB:  Q9BWJ5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 1
C
1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1 (SAP155)
Find proteins for O75533 (Homo sapiens)
Go to Gene View: SF3B1
Go to UniProtKB:  O75533
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PHD finger-like domain-containing protein 5A
D
85Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
Go to Gene View: PHF5A
Go to UniProtKB:  Q7RTV0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 3
A
1223Homo sapiensMutation(s): 0 
Gene Names: SF3B3 (KIAA0017, SAP130)
Find proteins for Q15393 (Homo sapiens)
Go to Gene View: SF3B3
Go to UniProtKB:  Q15393
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
9B0
Query on 9B0

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Download CCD File 
C
[(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{R})-6-methyl-6-oxidanyl-7-[(2~{R},3~{R})-3-[(2~{R},3~{S})-3-oxidanylpentan-2-yl]oxiran-2-yl]hepta-2,4-dien-2-yl]-7,10-bis(oxidanyl)-12-oxidanylidene-1-oxacyclododec-4-en-6-yl] 4-cycloheptylpiperazine-1-carboxylate
C40 H66 N2 O9
MNOMBFWMICHMKG-MGYWSNOQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China31650110470

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-11-06
    Type: Data collection, Other