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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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

  • 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 ...

    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

    H3 Biomedicine, Inc., Cambridge, MA 03129, USA.,Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. Electronic address: vladimir.pena@mpibpc.mpg.de.,Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 3
A
1209Homo sapiensMutation(s): 0 
Gene Names: SF3B3 (KIAA0017, SAP130)
Find proteins for Q15393 (Homo sapiens)
Go to Gene View: SF3B3
Go to UniProtKB:  Q15393
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 5
B
85Homo sapiensMutation(s): 0 
Gene Names: SF3B5 (SF3B10)
Find proteins for Q9BWJ5 (Homo sapiens)
Go to Gene View: SF3B5
Go to UniProtKB:  Q9BWJ5
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Splicing factor 3B subunit 1
C
852Homo sapiensMutation(s): 0 
Gene Names: SF3B1 (SAP155)
Find proteins for O75533 (Homo sapiens)
Go to Gene View: SF3B1
Go to UniProtKB:  O75533
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PHD finger-like domain-containing protein 5A
D
108Homo sapiensMutation(s): 0 
Gene Names: PHF5A
Find proteins for Q7RTV0 (Homo sapiens)
Go to Gene View: PHF5A
Go to UniProtKB:  Q7RTV0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BGZ
Query on BGZ

Download SDF File 
Download CCD File 
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
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 = 90.00
b = 154.568β = 90.00
c = 210.207γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-04 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Cretu, C., Pena, V.

Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History 

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