4Y97

Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Human Pol alpha B Subunit in Complex with the C-terminal Domain of the Catalytic Subunit.

Gu, J.Baranovskiy, A.G.Babayeva, N.D.Pavlov, Y.I.Tahirov, T.H.Suwa, Y.

(2015) J.Biol.Chem. 290: 14328-14337

  • DOI: 10.1074/jbc.M115.649954

  • PubMed Abstract: 
  • In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol δ and Pol ϵ. The C terminus of the Pol α catalytic subunit (p ...

    In eukaryotic DNA replication, short RNA-DNA hybrid primers synthesized by primase-DNA polymerase α (Prim-Pol α) are needed to start DNA replication by the replicative DNA polymerases, Pol δ and Pol ϵ. The C terminus of the Pol α catalytic subunit (p180C) in complex with the B subunit (p70) regulates the RNA priming and DNA polymerizing activities of Prim-Pol α. It tethers Pol α and primase, facilitating RNA primer handover from primase to Pol α. To understand these regulatory mechanisms and to reveal the details of human Pol α organization, we determined the crystal structure of p70 in complex with p180C. The structured portion of p70 includes a phosphodiesterase (PDE) domain and an oligonucleotide/oligosaccharide binding (OB) domain. The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. The p180C adopts an elongated asymmetric saddle shape, with a three-helix bundle in the middle and zinc-binding modules (Zn1 and Zn2) on each side. The extensive p180C-p70 interactions involve 20 hydrogen bonds and a number of hydrophobic interactions resulting in an extended buried surface of 4080 Å(2). Importantly, in the structure of the p180C-p70 complex with full-length p70, the residues from the N-terminal to the OB domain contribute to interactions with p180C. The comparative structural analysis revealed both the conserved features and the differences between the human and yeast Pol α complexes.


    Organizational Affiliation

    From the Eppley Institute for Research in Cancer and Allied Diseases and ttahirov@unmc.edu.,From the Eppley Institute for Research in Cancer and Allied Diseases and.,From the Eppley Institute for Research in Cancer and Allied Diseases and the Departments of Biochemistry and Molecular Biology and Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase alpha subunit B
A, C, E, G
598Homo sapiensMutation(s): 0 
Gene Names: POLA2
Find proteins for Q14181 (Homo sapiens)
Go to Gene View: POLA2
Go to UniProtKB:  Q14181
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase alpha catalytic subunit
B, D, F, H
180Homo sapiensMutation(s): 0 
Gene Names: POLA1 (POLA)
EC: 2.7.7.7
Find proteins for P09884 (Homo sapiens)
Go to Gene View: POLA1
Go to UniProtKB:  P09884
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B, D, F, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 103.593α = 90.00
b = 137.135β = 100.97
c = 132.092γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM101167

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-22
    Type: Database references
  • Version 1.2: 2015-06-17
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy