4RR2

Crystal structure of human primase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the human primase.

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

(2015) J.Biol.Chem. 290: 5635-5646

  • DOI: 10.1074/jbc.M114.624742

  • PubMed Abstract: 
  • DNA replication in bacteria and eukaryotes requires the activity of DNA primase, a DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large ...

    DNA replication in bacteria and eukaryotes requires the activity of DNA primase, a DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for RNA primer synthesis. Understanding of RNA synthesis priming in eukaryotes is currently limited due to the lack of crystal structures of the full-length primase and its complexes with substrates in initiation and elongation states. Here we report the crystal structure of the full-length human primase, revealing the precise overall organization of the enzyme, the relative positions of its functional domains, and the mode of its interaction with modeled DNA and RNA. The structure indicates that the dramatic conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis. The presence of a long linker between the N- and C-terminal domains of p58 provides the structural basis for the bulk of enzyme's conformational flexibility. Deletion of most of this linker affected the initiation and elongation steps of the primer synthesis.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA primase small subunit
A, C
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, D
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
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: 2.65 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.229 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 86.195α = 93.82
b = 88.899β = 96.57
c = 94.682γ = 111.72
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
CNSrefinement
HKL-2000data scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Database references