PDBsum entry 2py9

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protein dna_rna Protein-protein interface(s) links
RNA and DNA binding protein/RNA PDB id
Protein chains
72 a.a. *
Waters ×51
* Residue conservation analysis
PDB id:
Name: RNA and DNA binding protein/RNA
Title: Protein-RNA interaction involving kh1 domain from human poly(c)-binding protein-2
Structure: 12-mer c-rich strand of human telomeric RNA. Chain: e, f. Engineered: yes. Poly(rc)-binding protein 2. Chain: a, b, c, d. Synonym: alpha-cp2, hnrnp-e2. Engineered: yes
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: pcbp2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.56Å     R-factor:   0.220     R-free:   0.269
Authors: T.L.James,Z.Du,J.K.Lee
Key ref: Z.Du et al. (2007). X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2. RNA, 13, 1043-1051. PubMed id: 17526645
15-May-07     Release date:   12-Jun-07    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 72 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA binding     1 term  


RNA 13:1043-1051 (2007)
PubMed id: 17526645  
X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2.
Z.Du, J.K.Lee, S.Fenn, R.Tjhen, R.M.Stroud, T.L.James.
Poly(C)-binding proteins (PCBPs) are KH (hnRNP K homology) domain-containing proteins that recognize poly(C) DNA and RNA sequences in mammalian cells. Binding poly(C) sequences via the KH domains is critical for PCBP functions. To reveal the mechanisms of KH domain-D/RNA recognition and its functional importance, we have determined the crystal structures of PCBP2 KH1 domain in complex with a 12-nucleotide DNA corresponding to two repeats of the human C-rich strand telomeric DNA and its RNA equivalent. The crystal structures reveal molecular details for not only KH1-DNA/RNA interaction but also protein-protein interaction between two KH1 domains. NMR studies on a protein construct containing two KH domains (KH1 + KH2) of PCBP2 indicate that KH1 interacts with KH2 in a way similar to the KH1-KH1 interaction. The crystal structures and NMR data suggest possible ways by which binding certain nucleic acid targets containing tandem poly(C) motifs may induce structural rearrangement of the KH domains in PCBPs; such structural rearrangement may be crucial for some PCBP functions.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20080952 J.A.Chao, Y.Patskovsky, V.Patel, M.Levy, S.C.Almo, and R.H.Singer (2010).
ZBP1 recognition of beta-actin zipcode induces RNA looping.
  Genes Dev, 24, 148-158.
PDB code: 3krm
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
18252259 A.Spear, N.Sharma, and J.B.Flanegan (2008).
Protein-RNA tethering: the role of poly(C) binding protein 2 in poliovirus RNA replication.
  Virology, 374, 280-291.  
18656221 P.Sean, J.H.Nguyen, and B.L.Semler (2008).
The linker domain of poly(rC) binding protein 2 is a major determinant in poliovirus cap-independent translation.
  Virology, 378, 243-253.  
18422648 R.Valverde, L.Edwards, and L.Regan (2008).
Structure and function of KH domains.
  FEBS J, 275, 2712-2726.  
18701464 Z.Du, S.Fenn, R.Tjhen, and T.L.James (2008).
Structure of a construct of a human poly(C)-binding protein containing the first and second KH domains reveals insights into its regulatory mechanisms.
  J Biol Chem, 283, 28757-28766.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.