Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10312.55 
• Atom Count: 714 
• Residue Count: 83 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2P2R

Crystal structure of the third KH domain of human Poly(C)-Binding Protein-2 in complex with C-rich strand of human telomeric DNA

• DOI: 10.2210/pdb2P2R/pdb
• NDB: PD0977

• Classification: RNA AND DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2007-03-07 Released: 2007-06-12 
• Deposition Author(s): James, T.L., Stroud, R.M., Du, Z., Fenn, S., Tjhen, R., Lee, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 

Literature

Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution.

Fenn, S., Du, Z., Lee, J.K., Tjhen, R., Stroud, R.M., James, T.L.

(2007) Nucleic Acids Res. 35: 2651-2660

• PubMed: 17426136 
• DOI: 10.1093/nar/gkm139


• PubMed Abstract: 
  

KH (hnRNP K homology) domains, consisting of approximately 70 amino acid residues, are present in a variety of nucleic-acid-binding proteins. Among these are poly(C)-binding proteins (PCBPs), which are important regulators of mRNA stability and posttranscriptional regulation in general. All PCBPs contain three different KH domains and recognize poly(C)-sequences with high affinity and specificity. To reveal the molecular basis of poly(C)-sequence recognition, we have determined the crystal structure, at 1.6 A resolution, of PCBP2 KH3 domain in complex with a 7-nt DNA sequence (5'-AACCCTA-3') corresponding to one repeat of the C-rich strand of human telomeric DNA. The domain assumes a type-I KH fold in a betaalphaalphabetabetaalpha configuration. The protein-DNA interface could be studied in unprecedented detail and is made up of a series of direct and water-mediated hydrogen bonds between the protein and the DNA, revealing an especially dense network involving several structural water molecules for the last 2 nt in the core recognition sequence. Unlike published KH domain structures, the protein crystallizes without protein-protein contacts, yielding new insights into the dimerization properties of different KH domains. A nucleotide platform, an interesting feature found in some RNA molecules, was identified, evidently for the first time in DNA.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143-2280, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Poly(rC)-binding protein 2	A	76	Homo sapiens	Mutation(s): 0  Gene Names: PCBP2
Find proteins for Q15366 (Homo sapiens) Go to Gene View: PCBP2 Go to UniProtKB:  Q15366

Entity ID: 1
Molecule	Chains	Length	Organism
C-rich strand of human telomeric DNA	B	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CYT	A	6-AMINOPYRIMIDIN-2(1H)-ONE CYTOSINE C4 H5 N3 O OPTASPLRGRRNAP-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.242 
• R-Value Work: 0.205 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 81.069	α = 90.00
b = 81.069	β = 90.00
c = 87.815	γ = 120.00

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
HKL-2000	data scaling
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-07 
• Released Date: 2007-06-12 
• Deposition Author(s): James, T.L., Stroud, R.M., Du, Z., Fenn, S., Tjhen, R., Lee, J.K.

Revision History 

• Version 1.0: 2007-06-12
  Type: Initial release
• Version 1.1: 2007-10-16
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Advisory, Refinement description
• Version 1.4: 2019-07-24
  Type: Data collection, Derived calculations, Refinement description