4BPX

Crystal structure of human primase in complex with the primase- binding motif of DNA polymerase alpha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Human Primase Reveal Design of Nucleotide Elongation Site and Mode of Pol Alpha Tethering

Kilkenny, M.L.Longo, M.Perera, R.L.Pellegrini, L.

(2013) Proc.Natl.Acad.Sci.USA 110: 15961

  • DOI: 10.1073/pnas.1311185110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Initiation of DNA synthesis in genomic duplication depends on primase, the DNA-dependent RNA polymerase that synthesizes de novo the oligonucleotides that prime DNA replication. Due to the discontinuous nature of DNA replication, primase activity on ...

    Initiation of DNA synthesis in genomic duplication depends on primase, the DNA-dependent RNA polymerase that synthesizes de novo the oligonucleotides that prime DNA replication. Due to the discontinuous nature of DNA replication, primase activity on the lagging strand is required throughout the replication process. In eukaryotic cells, the presence of primase at the replication fork is secured by its physical association with DNA polymerase α (Pol α), which extends the RNA primer with deoxynucleotides. Our knowledge of the mechanism that primes DNA synthesis is very limited, as structural information for the eukaryotic enzyme has proved difficult to obtain. Here, we describe the crystal structure of human primase in heterodimeric form consisting of full-length catalytic subunit and a C-terminally truncated large subunit. We exploit the crystallographic model to define the architecture of its nucleotide elongation site and to show that the small subunit integrates primer initiation and elongation within the same set of functional residues. Furthermore, we define in atomic detail the mode of association of primase to Pol α, the critical interaction that keeps primase tethered to the eukaryotic replisome.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA PRIMASE SMALL SUBUNIT
A, C
423Homo sapiensMutation(s): 2 
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 POLYMERASE ALPHA CATALYTIC SUBUNIT, DNA PRIMASE LARGE SUBUNIT
B, D
269Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 120.680α = 90.00
b = 70.701β = 105.83
c = 127.160γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection