5N35

Gadolinium phased PBP2 (SSO6202) at 2.2 Ang


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme.

Yan, J.Beattie, T.R.Rojas, A.L.Schermerhorn, K.Gristwood, T.Trinidad, J.C.Albers, S.V.Roversi, P.Gardner, A.F.Abrescia, N.G.A.Bell, S.D.

(2017) Nat Commun 8: 15075-15075

  • DOI: https://doi.org/10.1038/ncomms15075
  • Primary Citation of Related Structures:  
    5N35, 5N41

  • PubMed Abstract: 

    Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. This contrasts with the multi-subunit B-family replicative polymerases of eukaryotes. Here we reveal that the highly studied PolB1 from Sulfolobus solfataricus exists as a heterotrimeric complex in cell extracts. Two small subunits, PBP1 and PBP2, associate with distinct surfaces of the larger catalytic subunit and influence the enzymatic properties of the DNA polymerase. Thus, multi-subunit replicative DNA polymerase holoenzymes are present in all three domains of life. We reveal the architecture of the assembly by a combination of cross-linking coupled with mass spectrometry, X-ray crystallography and single-particle electron microscopy. The small subunits stabilize the holoenzyme assembly and the acidic tail of one small subunit mitigates the ability of the enzyme to perform strand-displacement synthesis, with important implications for lagging strand DNA synthesis.


  • Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, Indiana University, Simon Hall MSB, 212 S Hawthorne Dr, Bloomington, Indiana 47405, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PolB1 Binding Protein 2 (PBP2)76Saccharolobus solfataricusMutation(s): 0 
Gene Names: SSOP1_0579SULA_1676SULB_1677SULC_1675
UniProt
Find proteins for A0A0E3GTJ4 (Saccharolobus solfataricus)
Explore A0A0E3GTJ4 
Go to UniProtKB:  A0A0E3GTJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3GTJ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.15α = 90
b = 62.15β = 90
c = 35.68γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MINECOSpainBFU2015-64541-R

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Structure summary