6GX9

Crystal structure of the TNPO3 - CPSF6 RSLD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6.

Jang, S.Cook, N.J.Pye, V.E.Bedwell, G.J.Dudek, A.M.Singh, P.K.Cherepanov, P.Engelman, A.N.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz206

  • PubMed Abstract: 
  • Cleavage factor I mammalian (CFIm) complex, composed of cleavage and polyadenylation specificity factor 5 (CPSF5) and serine/arginine-like protein CPSF6, regulates alternative polyadenylation (APA). Loss of CFIm function results in proximal polyadeny ...

    Cleavage factor I mammalian (CFIm) complex, composed of cleavage and polyadenylation specificity factor 5 (CPSF5) and serine/arginine-like protein CPSF6, regulates alternative polyadenylation (APA). Loss of CFIm function results in proximal polyadenylation site usage, shortening mRNA 3' untranslated regions (UTRs). Although CPSF6 plays additional roles in human disease, its nuclear translocation mechanism remains unresolved. Two β-karyopherins, transportin (TNPO) 1 and TNPO3, can bind CPSF6 in vitro, and we demonstrate here that while the TNPO1 binding site is dispensable for CPSF6 nuclear import, the arginine/serine (RS)-like domain (RSLD) that mediates TNPO3 binding is critical. The crystal structure of the RSLD-TNPO3 complex revealed potential CPSF6 interaction residues, which were confirmed to mediate TNPO3 binding and CPSF6 nuclear import. Both binding and nuclear import were independent of RSLD phosphorylation, though a hyperphosphorylated mimetic mutant failed to bind TNPO3 and mislocalized to the cell cytoplasm. Although hypophosphorylated CPSF6 largely supported normal polyadenylation site usage, a significant number of mRNAs harbored unnaturally extended 3' UTRs, similar to what is observed when other APA regulators, such as CFIIm component proteins, are depleted. Our results clarify the mechanism of CPSF6 nuclear import and highlight differential roles for RSLD phosphorylation in nuclear translocation versus regulation of APA.


    Organizational Affiliation

    Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transportin-3
A, B
923Homo sapiensMutation(s): 0 
Gene Names: TNPO3 (IPO12)
Find proteins for Q9Y5L0 (Homo sapiens)
Go to Gene View: TNPO3
Go to UniProtKB:  Q9Y5L0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cleavage and polyadenylation specificity factor subunit 6
C, D
70Homo sapiensMutation(s): 0 
Gene Names: CPSF6 (CFIM68)
Find proteins for Q16630 (Homo sapiens)
Go to Gene View: CPSF6
Go to UniProtKB:  Q16630
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCN
Query on BCN

Download SDF File 
Download CCD File 
A, B
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN

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Download CCD File 
A, B
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.214 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 200.335α = 90.00
b = 200.335β = 90.00
c = 234.807γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesGM082251

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-10
    Type: Data collection, Database references