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 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.60 kDa 
• Atom Count: 3781 
• Residue Count: 412 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

3MDI

Crystal Structure of the 25kDa Subunit of Human Cleavage factor Im in complex with RNA UGUAAA

• DOI: 10.2210/pdb3MDI/pdb
• NDB: NA0511

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


• Deposited: 2010-03-30 Released: 2010-06-02 
• Deposition Author(s): Yang, Q., Gilmartin, G.M., Doublie, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.233 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Literature

Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.

Yang, Q., Gilmartin, G.M., Doublie, S.

(2010) Proc Natl Acad Sci U S A 107: 10062-10067

• PubMed: 20479262 
• DOI: 10.1073/pnas.1000848107
• Primary Citation of Related Structures:  
  3MDG, 3MDI


• PubMed Abstract: 
  

Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI(m)25) of the CFI(m) complex possesses a characteristic alpha/beta/alpha Nudix fold, CFI(m)25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI(m)25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI(m)25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.

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Organizational Affiliation: 

Department of Microbiology and Molecular Genetics, Stafford Hall, 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, B	227	Homo sapiens	Mutation(s): 0  Gene Names: CFIM25, CPSF25, CPSF5, NUDT21
Find proteins for O43809 (Homo sapiens) Explore O43809  Go to UniProtKB:  O43809
NIH Common Fund Data Resources
PHAROS:  O43809 GTEx:  ENSG00000167005

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*GP*UP*AP*AP*A)-3')	C	6	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.233 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.362	α = 90
b = 72.037	β = 90
c = 96.16	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-30 
• Released Date: 2010-06-02 
Deposition Author(s): Yang, Q., Gilmartin, G.M., Doublie, S.

Revision History 

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance