5IFE

Crystal structure of the human SF3b core complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    5HY7, 5IFE

  • 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) 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 ...

    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. Electronic address: vladimir.pena@mpibpc.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 5A [auth B]86Homo sapiensMutation(s): 0 
Gene Names: SF3B5, SF3B10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWJ5 (Homo sapiens)
Explore Q9BWJ5 
Go to UniProtKB:  Q9BWJ5
PHAROS:  Q9BWJ5
GTEx:  ENSG00000169976 
Entity Groups  
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UniProt GroupQ9BWJ5
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 1B [auth C]1304Homo sapiensMutation(s): 0 
Gene Names: SF3B1, SAP155
UniProt & NIH Common Fund Data Resources
Find proteins for O75533 (Homo sapiens)
Explore O75533 
Go to UniProtKB:  O75533
PHAROS:  O75533
GTEx:  ENSG00000115524 
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UniProt GroupO75533
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger-like domain-containing protein 5AC [auth D]120Homo sapiensMutation(s): 0 
Gene Names: PHF5A
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Find proteins for Q7RTV0 (Homo sapiens)
Explore Q7RTV0 
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PHAROS:  Q7RTV0
GTEx:  ENSG00000100410 
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UniProt GroupQ7RTV0
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Splicing factor 3B subunit 3D [auth A]1235Homo sapiensMutation(s): 0 
Gene Names: SF3B3, KIAA0017, SAP130
UniProt & NIH Common Fund Data Resources
Find proteins for Q15393 (Homo sapiens)
Explore Q15393 
Go to UniProtKB:  Q15393
PHAROS:  Q15393
GTEx:  ENSG00000189091 
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UniProt GroupQ15393
Protein Feature View
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
K
Query on K
Download Ideal Coordinates CCD File 
H [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.055α = 90
b = 154.436β = 90
c = 210.418γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection