5EXR

Crystal structure of human primosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.4 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase small subunit
A, E
420Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7.-
Find proteins for P49642 (Homo sapiens)
Go to Gene View: PRIM1
Go to UniProtKB:  P49642
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA primase large subunit
B, F
509Homo 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: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase alpha catalytic subunit
C, G
1128Homo sapiensMutation(s): 1 
Gene Names: POLA1 (POLA)
EC: 2.7.7.7
Find proteins for P09884 (Homo sapiens)
Go to Gene View: POLA1
Go to UniProtKB:  P09884
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase alpha subunit B
D, H
597Homo sapiensMutation(s): 0 
Gene Names: POLA2
Find proteins for Q14181 (Homo sapiens)
Go to Gene View: POLA2
Go to UniProtKB:  Q14181
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

Download SDF File 
Download CCD File 
A, C, E, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.268 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 113.096α = 90.00
b = 210.164β = 93.56
c = 172.565γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
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 SciencesUnited StatesGM101167
National Institutes of Health/National Institute of General Medical SciencesUnited 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