PDBsum entry 2cl3

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protein links
Nuclear protein PDB id
Protein chain
202 a.a. *
Waters ×216
* Residue conservation analysis
PDB id:
Name: Nuclear protein
Title: Crystal structure of human cleavage and polyadenylation specificity factor 5 (cpsf5)
Structure: Cleavage and polyadenylation specificity factor 5. Chain: a. Synonym: cleavage and polyadenylation specificity factor 25 kda subunit, cpsf 25 kda subunit, pre-mRNA cleavage factor im 25-kda subunit, nucleoside diphosphate-linked moiety x motif 21, nudix motif 21. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
1.90Å     R-factor:   0.171     R-free:   0.207
Authors: P.Stenmark,M.Hogbom,C.Arrowsmith,H.Berglund,R.Collins, A.Edwards,M.Ehn,S.Flodin,A.Flores,S.Graslund,M.Hammarstrom, B.M.Hallberg,L.Holmberg Schiavone,T.Kotenyova, A.Magnusdottir,P.Nilsson-Ehle,T.Nyman,D.Ogg,C.Persson, J.Sagemark,M.Sundstrom,A.G.Thorsell,S.Van Den Berg, K.Wallden,J.Weigelt,P.Nordlund
Key ref:
L.Trésaugues et al. (2008). The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site. Proteins, 73, 1047-1052. PubMed id: 18767156 DOI: 10.1002/prot.22198
25-Apr-06     Release date:   04-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O43809  (CPSF5_HUMAN) -  Cleavage and polyadenylation specificity factor subunit 5
227 a.a.
202 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   5 terms 
  Biological process     gene expression   9 terms 
  Biochemical function     protein binding     7 terms  


DOI no: 10.1002/prot.22198 Proteins 73:1047-1052 (2008)
PubMed id: 18767156  
The crystal structure of human cleavage and polyadenylation specific factor-5 reveals a dimeric Nudix protein with a conserved catalytic site.
L.Trésaugues, P.Stenmark, H.Schüler, S.Flodin, M.Welin, T.Nyman, M.Hammarström, M.Moche, S.Gräslund, P.Nordlund.
No abstract given.

  Selected figure(s)  
Figure 1.
Figure 1. (a) Structure of the CPSF5 dimer (SO[4]-bound form). Nudix fold and additional secondary structure elements are colored respectively in cyan and blue for one monomer and purple and red for the other. Atoms of the sulfate ions are shown as spheres. The flexible Phe103 side chain is shown as a stick model with carbons colored in orange. The N-terminal peptides forming crystal interactions with the 2- 9 surfaces are also shown as a C trace, the C and the nitrogen of their N-terminal residue being shown as spheres (residues 21-32 of the apo form in green, and residues 22-32 of the SO[4]-bound form in yellow). (b) Sequence of the constructs 1 and 2. The sequence of human CPSF5 is depicted, the sequence of constructs 1 and 2 being boxed in red and green respectively.
Figure 3.
Figure 3. Molecular surface representation around the sulfate-binding site including residues potentially involved in catalysis or recognition. Glu170 provides second sphere stabilization of Arg150. Negatively and positively charged potentials are colored in red and blue, respectively. Tube representation of the C -trace of CPSF5 is colored in green. Conserved polar residues in the channel are represented as stick models. Atoms of the sulfate ion are shown as balls.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 1047-1052) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21295486 Q.Yang, M.Coseno, G.M.Gilmartin, and S.Doublié (2011).
Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping.
  Structure, 19, 368-377.
PDB codes: 3q2s 3q2t
20479262 Q.Yang, G.M.Gilmartin, and S.Doublié (2010).
Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.
  Proc Natl Acad Sci U S A, 107, 10062-10067.
PDB codes: 3mdg 3mdi
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