1ZZI | pdb_00001zzi

Crystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA

• PDB DOI: https://doi.org/10.2210/pdb1ZZI/pdb
• NAKB: 1ZZI

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


• Deposited: 2005-06-14 Released: 2005-08-09 
• Deposition Author(s): Backe, P.H., Messias, A.C., Ravelli, R.B., Sattler, M., Cusack, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

X-Ray Crystallographic and NMR Studies of the Third KH Domain of hnRNP K in Complex with Single-Stranded Nucleic Acids

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

(2005) Structure 13: 1055-1067

• PubMed: 16004877 
• DOI: https://doi.org/10.1016/j.str.2005.04.008
• Primary Citation Related Structures: 
  1ZZI, 1ZZJ, 1ZZK


• PubMed 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.

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Organizational Affiliation: 
• Grenoble Outstation, European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, F-38042 Grenoble Cedex 9, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.23 kDa 
• Atom Count: 1,589 
• Modeled Residue Count: 173 
• Deposited Residue Count: 176 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoprotein K	C [auth A], D [auth B]	82	Homo sapiens	Mutation(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 ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*CP*CP*CP*C)-3'	A [auth C], B [auth D]	6	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.240 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.59	α = 90
b = 52.59	β = 90
c = 104.891	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-09 
Deposition Author(s): Backe, P.H., Messias, A.C., Ravelli, R.B., Sattler, M., Cusack, S.

Revision History  

• Version 1.0: 2005-08-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references