7K95

Crystal structure of human CPSF30 in complex with hFip1

  • Classification: NUCLEAR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-09-28 Released: 2020-11-11 
  • Deposition Author(s): Hamilton, K., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism for the interaction between human CPSF30 and hFip1.

Hamilton, K.Tong, L.

(2020) Genes Dev 34: 1753-1761

  • DOI: https://doi.org/10.1101/gad.343814.120
  • Primary Citation of Related Structures:  
    7K95

  • PubMed Abstract: 

    Most eukaryotic pre-mRNAs must undergo 3'-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3'-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2-ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4-ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4-ZF5 in complex with residues 161-200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30-hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a K d of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30-hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, New York 10027, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Cleavage and polyadenylation specificity factor subunit 460Homo sapiensMutation(s): 0 
Gene Names: CPSF4CPSF30NARNEB1
UniProt & NIH Common Fund Data Resources
Find proteins for O95639 (Homo sapiens)
Explore O95639 
Go to UniProtKB:  O95639
PHAROS:  O95639
GTEx:  ENSG00000160917 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95639
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA 3'-end-processing factor FIP1
B, C
42Homo sapiensMutation(s): 0 
Gene Names: FIP1L1FIP1RHE
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UN15 (Homo sapiens)
Explore Q6UN15 
Go to UniProtKB:  Q6UN15
PHAROS:  Q6UN15
GTEx:  ENSG00000145216 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UN15
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.04α = 90
b = 79.04β = 90
c = 48.662γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesR35GM118093

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2020-12-16
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references