6EN4

SF3b core in complex with a splicing modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 

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Literature

Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds.

Cretu, C.Agrawal, A.A.Cook, A.Will, C.L.Fekkes, P.Smith, P.G.Luhrmann, R.Larsen, N.Buonamici, S.Pena, V.

(2018) Mol Cell 70: 265-273.e8

  • DOI: 10.1016/j.molcel.2018.03.011
  • Primary Citation of Related Structures:  
    6EN4

  • PubMed Abstract: 
  • SF3B is a multi-protein complex essential for branch site (BS) recognition and selection during pre-mRNA splicing. Several splicing modulators with antitumor activity bind SF3B and thereby modulate splicing. Here we report the crystal structure of a human SF3B core in complex with pladienolide B (PB), a macrocyclic splicing modulator and potent inhibitor of tumor cell proliferation ...

    SF3B is a multi-protein complex essential for branch site (BS) recognition and selection during pre-mRNA splicing. Several splicing modulators with antitumor activity bind SF3B and thereby modulate splicing. Here we report the crystal structure of a human SF3B core in complex with pladienolide B (PB), a macrocyclic splicing modulator and potent inhibitor of tumor cell proliferation. PB stalls SF3B in an open conformation by acting like a wedge within a hinge, modulating SF3B's transition to the closed conformation needed to form the BS adenosine-binding pocket and stably accommodate the BS/U2 duplex. This work explains the structural basis for the splicing modulation activity of PB and related compounds, and reveals key interactions between SF3B and a common pharmacophore, providing a framework for future structure-based drug design.


    Organizational Affiliation

    Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: vladimir.pena@mpibpc.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3A1,209Homo sapiensMutation(s): 0 
Gene Names: SF3B3KIAA0017SAP130
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Find proteins for Q15393 (Homo sapiens)
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Go to UniProtKB:  Q15393
PHAROS:  Q15393
Entity Groups  
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UniProt GroupQ15393
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5B85Homo sapiensMutation(s): 0 
Gene Names: SF3B5SF3B10
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Find proteins for Q9BWJ5 (Homo sapiens)
Explore Q9BWJ5 
Go to UniProtKB:  Q9BWJ5
PHAROS:  Q9BWJ5
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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
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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
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Find proteins for Q7RTV0 (Homo sapiens)
Explore Q7RTV0 
Go to UniProtKB:  Q7RTV0
PHAROS:  Q7RTV0
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UniProt GroupQ7RTV0
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGZ
Query on BGZ

Download Ideal Coordinates CCD File 
H [auth D][(2~{S},3~{S},4~{E},6~{S},7~{R},10~{R})-3,7-dimethyl-2-[(2~{E},4~{E},6~{S})-6-methyl-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] ethanoate
C30 H48 O8
SDOUORKJIJYJNW-QHOUZYGJSA-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
Binding Affinity Annotations 
IDSourceBinding Affinity
BGZ BindingDB:  6EN4 EC50: min: 0.86, max: 1 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.067α = 90
b = 154.568β = 90
c = 210.207γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release