Macromolecule Content

• Total Structure Weight: 12.61 kDa 
• Atom Count: 671 
• Modelled Residue Count: 81 
• Deposited Residue Count: 99 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1J5K

COMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED 10MER DNA OLIGONUCLEOTIDE

• DOI: 10.2210/pdb1J5K/pdb
• NDB: 1J5K

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


• Deposited: 2002-05-13 Released: 2002-07-10 
• Deposition Author(s): Clore, G.M., Braddock, D.T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 125 
• Conformers Submitted: 1 
• Selection Criteria: REGULARIZED MEAN STRUCTURE 

Literature

Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA.

Braddock, D.T., Baber, J.L., Levens, D., Clore, G.M.

(2002) EMBO J 21: 3476-3485

• PubMed: 12093748 
• DOI: 10.1093/emboj/cdf352
• Primary Citation of Related Structures:  
  1J5K


• PubMed Abstract: 
  

To elucidate the basis of sequence-specific single-stranded (ss) DNA recognition by K homology (KH) domains, we have solved the solution structure of a complex between the KH3 domain of the transcriptional regulator heterogeneous nuclear ribonucleoprotein K (hnRNP K) and a 10mer ssDNA. We show that hnRNP K KH3 specifically recognizes a tetrad of sequence 5'd-TCCC. The complex is stabilized by a dense network of methyl-oxygen hydrogen bonds involving the methyl groups of three isoleucine residues and the O2 and N3 atoms of the two central cytosine bases. Comparison with the recently solved structure of a specific protein-ssDNA complex involving the KH3 and KH4 domains of the far upstream element (FUSE) binding protein FBP suggests that the amino acid located five residues N-terminal of the invariant GXXG motif, which is characteristic of all KH domains, plays a crucial role in discrimination of the first two bases of the tetrad.

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Organizational Affiliation: 

Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0510, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoprotein K	B [auth A]	89	Homo sapiens	Mutation(s): 0  Gene Names: HNRNPK, HNRPK
Find proteins for P61978 (Homo sapiens) Explore P61978  Go to UniProtKB:  P61978
NIH Common Fund Data Resources
PHAROS:  P61978 GTEx:  ENSG00000165119

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*AP*T*TP*CP*CP*CP*TP*C)-3'	A [auth B]	10	N/A

Small Molecules

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DNA	Kd :  3000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 125 
• Conformers Submitted: 1 
• Selection Criteria: REGULARIZED MEAN STRUCTURE 
• OLDERADO: 1J5K Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-13 
• Released Date: 2002-07-10 
Deposition Author(s): Clore, G.M., Braddock, D.T.

Revision History  

• Version 1.0: 2002-07-10
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance