1J5K

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


Experimental Data Snapshot

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

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This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heterogeneous nuclear ribonucleoprotein KB [auth A]89Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61978 (Homo sapiens)
Explore P61978 
Go to UniProtKB:  P61978
PHAROS:  P61978
GTEx:  ENSG00000165119 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61978
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*TP*AP*T*TP*CP*CP*CP*TP*C)-3'A [auth B]10N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1J5K Kd: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection