PDBsum entry: 1zzi

Structural protein/DNA

PDB id: 1zzi

Contents

Protein chains

82 a.a. *

DNA/RNA

Waters ×136

* Residue conservation analysis

PDB id:

1zzi

Name:

Structural protein/DNA

Title:

Crystal structure analysis of the third kh domain of hnrnp k complex with ssdna

Structure:

5'-d( Cp Tp Cp Cp Cp C)-3'. Chain: c, d. Engineered: yes. Heterogeneous nuclear ribonucleoprotein k. Chain: a, b. Fragment: kh3 domain. Synonym: hnrnp k, transformation up-regulated nuclear prote engineered: yes

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.197 R-free: 0.240

Authors:

P.H.Backe,A.C.Messias,R.B.Ravelli,M.Sattler,S.Cusack

Key ref:

P.H.Backe et al. (2005). X-ray crystallographic and NMR studies of the third KH domain of hnRNP K in complex with single-stranded nucleic acids. Structure, 13, 1055-1067. PubMed id: 16004877 DOI: 10.1016/j.str.2005.04.008

Date:

14-Jun-05 Release date: 09-Aug-05

Protein chains

P61978  (HNRPK_HUMAN) -  Heterogeneous nuclear ribonucleoprotein K

Seq: 463 a.a.

Struc: 82 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biochemical function: RNA binding (1 term)

DOI no: 10.1016/j.str.2005.04.008

Structure 13:1055-1067 (2005)

PubMed id: 16004877

X-ray crystallographic and NMR studies of the third KH domain of hnRNP K in complex with single-stranded nucleic acids.

P.H.Backe, A.C.Messias, R.B.Ravelli, M.Sattler, S.Cusack.

ABSTRACT

The heterogeneous nuclear ribonucleoprotein (hnRNP) K is implicated in multiple functions in the regulation of gene expression and acts as a hub at the intersection of signaling pathways and processes involving nucleic acids. Central to its function is its ability to bind both ssDNA and ssRNA via its KH (hnRNP K homology) domains. We determined crystal structures of hnRNP K KH3 domain complexed with 15-mer and 6-mer (CTC(4)) ssDNAs at 2.4 and 1.8 A resolution, respectively, and show that the KH3 domain binds specifically to both TCCC and CCCC sequences. In parallel, we used NMR to compare the binding affinity and mode of interaction of the KH3 domain with several ssRNA ligands and CTC(4) ssDNA. Based on a structure alignment of the KH3-CTC(4) complex with known structures of other KH domains in complex with ssRNA, we discuss recognition of tetranucleotide sequences by KH domains.

Selected figure(s)

Figure 2.
Figure 2. Detailed View of the KH3-CTC[4] Complex
(A) Stereo diagram showing conserved conformation of the central tetranucleotide in the two examples of the KH3-CTC[4] complex.
(B) Stereo view showing how Gly400 and Ile403 are inserted like a wedge, preventing the base stacking of Thy2, Cyt3, and Cyt4.
(C) sA-weighted 2F[o] - F[c] electron density contoured at 1.0 s (blue) showing the recognition of the first nucleotide, thymine, in the core recognition sequence.
(D) sA-weighted 2F[o] - F[c] electron density contoured at 1.0 s (blue) of the interactions of the two middle nucleotides (Cyt3 and Cyt4) in the core recognition sequence with the protein.
(E) Stereo view showing the water-mediated hydrogen bonds and base stacking of Cyt5. Water molecules are indicated as red spheres, and hydrogen bonds are indicated as green dashed lines.

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1055-1067) copyright 2005.

Figure was selected by an automated process.