7ZY4

Crystal structure of human CstF77 in complex with hFip1

• PDB DOI:  https://doi.org/10.2210/pdb7ZY4/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-23 Released: 2022-09-14 
• Deposition Author(s): Muckenfuss, L.M., Jinek, M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.247 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Literature

Fip1 is a multivalent interaction scaffold for processing factors in human mRNA 3' end biogenesis.

Muckenfuss, L.M., Migenda Herranz, A.C., Boneberg, F.M., Clerici, M., Jinek, M.

(2022) Elife 11

• PubMed: 36073787 
• DOI: https://doi.org/10.7554/eLife.80332
• Primary Citation of Related Structures:  
  7ZY4, 7ZYH


• PubMed Abstract: 
  

3' end formation of most eukaryotic mRNAs is dependent on the assembly of a ~1.5 megadalton multiprotein complex, that catalyzes the coupled reaction of pre-mRNA cleavage and polyadenylation. In mammals, the cleavage and polyadenylation specificity factor (CPSF) constitutes the core of the 3' end processing machinery onto which the remaining factors, including cleavage stimulation factor (CstF) and poly(A) polymerase (PAP), assemble. These interactions are mediated by Fip1, a CPSF subunit characterized by high degree of intrinsic disorder. Here, we report two crystal structures revealing the interactions of human Fip1 (hFip1) with CPSF30 and CstF77. We demonstrate that CPSF contains two copies of hFip1, each binding to the zinc finger (ZF) domains 4 and 5 of CPSF30. Using polyadenylation assays we show that the two hFip1 copies are functionally redundant in recruiting one copy of PAP, thereby increasing the processivity of RNA polyadenylation. We further show that the interaction between hFip1 and CstF77 is mediated via a short motif in the N-terminal 'acidic' region of hFip1. In turn, CstF77 competitively inhibits CPSF-dependent PAP recruitment and 3' polyadenylation. Taken together, these results provide a structural basis for the multivalent scaffolding and regulatory functions of hFip1 in 3' end processing.

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Organizational Affiliation: 

Department of Biochemistry, University of Zurich, Zurich, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 82.11 kDa 
• Atom Count: 5,297 
• Modelled Residue Count: 628 
• Deposited Residue Count: 700 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cleavage stimulation factor subunit 3	A, B	312	Homo sapiens	Mutation(s): 0  Gene Names: CSTF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q12996 (Homo sapiens) Explore Q12996  Go to UniProtKB:  Q12996
PHAROS:  Q12996

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
hFip1	C, D	38	Homo sapiens	Mutation(s): 0  Gene Names: FIP1L1, FIP1, RHE
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UN15 (Homo sapiens) Explore Q6UN15  Go to UniProtKB:  Q6UN15
PHAROS:  Q6UN15

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.247 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.612	α = 90
b = 157.612	β = 90
c = 161.005	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Muckenfuss, L.M., Jinek, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2022-09-21
  Changes: Database references