5EXR

Crystal structure of human primosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.268 

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:  
    5EXR, 5F0Q, 5F0S

  • 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 centers was an enigma for over three decades ...

    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 ttahirov@unmc.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA primase small subunitA, E420Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7 (PDB Primary Data), 2.7.7.102 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49642 (Homo sapiens)
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PHAROS:  P49642
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UniProt GroupP49642
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA primase large subunitB, F509Homo sapiensMutation(s): 0 
Gene Names: PRIM2, PRIM2A
EC: 2.7.7
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PHAROS:  P49643
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UniProt GroupP49643
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunitC, G1,128Homo sapiensMutation(s): 1 
Gene Names: POLA1, POLA
EC: 2.7.7.7
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Find proteins for P09884 (Homo sapiens)
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PHAROS:  P09884
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UniProt GroupP09884
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha subunit BD, H597Homo sapiensMutation(s): 0 
Gene Names: POLA2
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Find proteins for Q14181 (Homo sapiens)
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PHAROS:  Q14181
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UniProt GroupQ14181
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 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
b = 210.164β = 93.56
c = 172.565γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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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 Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103403

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2016-06-01
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence