Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.54 kDa 
• Atom Count: 1817 
• Residue Count: 203 
• Unique protein chains: 1

3BAP

Crystal Structure of the 25 kDa Subunit of Human Cleavage Factor Im

• DOI: 10.2210/pdb3BAP/pdb

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


• Deposited: 2007-11-08 Released: 2008-02-19 
• Deposition Author(s): Coseno, M., Doublie, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Crystal structure of the 25 kDa subunit of human cleavage factor Im.

Coseno, M., Martin, G., Berger, C., Gilmartin, G., Keller, W., Doublie, S.

(2008) Nucleic Acids Res 36: 3474-3483

• PubMed: 18445629 
• DOI: 10.1093/nar/gkn079
• Primary Citation of Related Structures:  
  3BAP, 3BHO


• PubMed Abstract: 
  

Cleavage factor I(m) is an essential component of the pre-messenger RNA 3'-end processing machinery in higher eukaryotes, participating in both the polyadenylation and cleavage steps. Cleavage factor I(m) is an oligomer composed of a small 25 kDa subunit (CF I(m)25) and a variable larger subunit of either 59, 68 or 72 kDa. The small subunit also interacts with RNA, poly(A) polymerase, and the nuclear poly(A)-binding protein. These protein-protein interactions are thought to be facilitated by the Nudix domain of CF I(m)25, a hydrolase motif with a characteristic alpha/beta/alpha fold and a conserved catalytic sequence or Nudix box. We present here the crystal structures of human CF I(m)25 in its free and diadenosine tetraphosphate (Ap(4)A) bound forms at 1.85 and 1.80 A, respectively. CF I(m)25 crystallizes as a dimer and presents the classical Nudix fold. Results from crystallographic and biochemical experiments suggest that CF I(m)25 makes use of its Nudix fold to bind but not hydrolyze ATP and Ap(4)A. The complex and apo protein structures provide insight into the active oligomeric state of CF I(m) and suggest a possible role of nucleotide binding in either the polyadenylation and/or cleavage steps of pre-messenger RNA 3'-end processing.

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Organizational Affiliation: 

Department of Microbiology and Department of Molecular Genetics, University of Vermont, Burlington, VT 05405, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cleavage and polyadenylation specificity factor subunit 5	A	227	Homo sapiens	Mutation(s): 0  Gene Names: NUDT21, CFIM25, CPSF25, CPSF5
Find proteins for O43809 (Homo sapiens) Explore O43809  Go to UniProtKB:  O43809
NIH Common Fund Data Resources
PHAROS:  O43809 GTEx:  ENSG00000167005

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.115	α = 90
b = 80.115	β = 90
c = 72.209	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-08 
• Released Date: 2008-02-19 
Deposition Author(s): Coseno, M., Doublie, S.

Revision History 

• Version 1.0: 2008-02-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary