5F0Q

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome.

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

(2016) J.Biol.Chem. 291: 10006-10020

  • DOI: 10.1074/jbc.M116.717405
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human primosome, a 340-kilodalton complex of primase and DNA polymerase α (Polα), synthesizes chimeric RNA-DNA primers to be extended by replicative DNA polymerases δ and ϵ. The intricate mechanism of concerted primer synthesis by two catalytic c ...

    The human primosome, a 340-kilodalton complex of primase and DNA polymerase α (Polα), synthesizes chimeric RNA-DNA primers to be extended by replicative DNA polymerases δ and ϵ. The intricate mechanism of concerted primer synthesis by two catalytic centers was an enigma for over three decades. Here we report the crystal structures of two key complexes, the human primosome and the C-terminal domain of the primase large subunit (p58C) with bound DNA/RNA duplex. These structures, along with analysis of primase/polymerase activities, provide a plausible mechanism for all transactions of the primosome including initiation, elongation, accurate counting of RNA primer length, primer transfer to Polα, and concerted autoregulation of alternate activation/inhibition of the catalytic centers. Our findings reveal a central role of p58C in the coordinated actions of two catalytic domains in the primosome and ultimately could impact the design of anticancer drugs.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase large subunit
A, B
191Homo sapiensMutation(s): 0 
Gene Names: PRIM2 (PRIM2A)
EC: 2.7.7.-
Find proteins for P49643 (Homo sapiens)
Go to Gene View: PRIM2
Go to UniProtKB:  P49643
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')C,E6Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')D,F12Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GTP
Query on GTP
C, E
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.223 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 122.507α = 90.00
b = 126.002β = 90.00
c = 83.942γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
CNSrefinement

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 Sciences (NIH/NIGMS)United StatesGM101167
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA036727
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Type: Database references
  • Version 1.2: 2016-06-01
    Type: Database references
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence
  • Version 1.5: 2019-12-04
    Type: Author supporting evidence