5IFE

Crystal structure of the human SF3b core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular Architecture of SF3b and Structural Consequences of Its Cancer-Related Mutations.

Cretu, C.Schmitzova, J.Ponce-Salvatierra, A.Dybkov, O.De Laurentiis, E.I.Sharma, K.Will, C.L.Urlaub, H.Luhrmann, R.Pena, V.

(2016) Mol.Cell 64: 307-319

  • DOI: 10.1016/j.molcel.2016.08.036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SF3b is a heptameric protein complex of the U2 small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. Mutations in the largest SF3b subunit, SF3B1/SF3b155, are linked to cancer and lead to alternative branch site (BS) select ...

    SF3b is a heptameric protein complex of the U2 small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. Mutations in the largest SF3b subunit, SF3B1/SF3b155, are linked to cancer and lead to alternative branch site (BS) selection. Here we report the crystal structure of a human SF3b core complex, revealing how the distinctive conformation of SF3b155's HEAT domain is maintained by multiple contacts with SF3b130, SF3b10, and SF3b14b. Protein-protein crosslinking enabled the localization of the BS-binding proteins p14 and U2AF65 within SF3b155's HEAT-repeat superhelix, which together with SF3b14b forms a composite RNA-binding platform. SF3b155 residues, the mutation of which leads to cancer, contribute to the tertiary structure of the HEAT superhelix and its surface properties in the proximity of p14 and U2AF65. The molecular architecture of SF3b reveals the spatial organization of cancer-related SF3b155 mutations and advances our understanding of their effects on SF3b structure and function.


    Organizational Affiliation

    Research Group Macromolecular Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Max Planck Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,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.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany.




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
120Homo 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
1235Homo 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 2 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

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.055α = 90.00
b = 154.436β = 90.00
c = 210.418γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
AutoSolphasing
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Germany--

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references