4QCL | pdb_00004qcl

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dCTP

• PDB DOI: https://doi.org/10.2210/pdb4QCL/pdb
• NAKB: 4QCL

• Classification: TRANSFERASE/DNA/RNA
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-05-12 Released: 2014-11-26 
• Deposition Author(s): Baranovskiy, A.G., Suwa, Y., Babayeva, N.D., Gu, J., Tahirov, T.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.239 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Activity and fidelity of human DNA polymerase alpha depend on primer structure

Baranovskiy, A.G., Duong, V., Babayeva, N.D., Zhang, Y., Pavlov, Y., Anderson, K., Tahirov, T.H.

(2018) J Biological Chem 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.56 kDa 
• Atom Count: 7,910 
• Modeled Residue Count: 889 
• Deposited Residue Count: 954 
• Unique protein chains: 1
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase alpha catalytic subunit	A	922	Homo sapiens	Mutation(s): 1  Gene Names: POLA, POLA1 EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for P09884 (Homo sapiens) Explore P09884  Go to UniProtKB:  P09884
PHAROS:  P09884 GTEx:  ENSG00000101868

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA PRIMER	B	11	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA TEMPLATE	C	21	N/A

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	D [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
1PE	I [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
ZN	F [auth A], G [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.239 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.763	α = 90
b = 140.763	β = 90
c = 181.315	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-26 
Deposition Author(s): Baranovskiy, A.G., Suwa, Y., Babayeva, N.D., Gu, J., Tahirov, T.H.

Revision History  

• Version 1.0: 2014-11-26
  Type: Initial release
  
• Version 1.1: 2018-03-14
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations