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Comment
. 2020 Oct 5;11(1):5000.
doi: 10.1038/s41467-020-18855-1.

Does PCNA diffusion on DNA follow a rotation-coupled translation mechanism?

Harry Mark Greenblatt  1 , Haim Rozenberg  1 , Dina Daitchman  1 , Yaakov Levy  2
Affiliations
Comment

Does PCNA diffusion on DNA follow a rotation-coupled translation mechanism?

Harry Mark Greenblatt et al. Nat Commun. .
No abstract available

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Assessment of the electron density of putative DNA in PDB 6GIS.
a Simulated annealing difference omit map (mFo-DFc), contoured at 2.0σ, overlaid with the model of DNA from the crystal structure, showing no evidence of DNA bound to the interior of PCNA. The DNA strand that interacts with the protein is colored yellow, and the complementary strand is colored orange. b Same difference map at 1.3σ. Note that the noisy density also covers parts of the protein, indicating that the contour level is too low, but still does not correspond to the DNA. c Polder omit map contoured at 1.3σ, showing copious density, but not corresponding to DNA, particularly on the lower left of the yellow strand, which purportedly interacts with PCNA. In order to generate an effective omit map, we removed the DNA (7.2% of the total atoms), and ran simulated annealing using PHENIX to decrease bias from the starting model. We also removed all TLS and NCS parameters, and used group B factors (2 values per residue, in consideration of the relatively low resolution: 2.82 Å), but no other adjustments were made to the model. This resulted in a significant drop in both Rwork (from 24.7 to 19.5%) and Rfree (from 28.4 to 24.9%), and the final geometry was also improved (RMSD bonds from 0.016 to 0.008Å, and RMSD angles from 1.8 to 1.0°), clearly indicating a large improvement in the model. The RMSD between the starting structure and the final structure was 0.51 Å for all protein atoms. In order to confirm that the improvement in Rwork and Rfree were not resulting from differences between Phenix and REFMAC, the output from Phenix was run through REFMAC, giving a final R-work of 19.1%, and Rfree of 24.6%. d Simulated annealing difference omit map, for 3BEP, contoured at 2σ. Images made in PyMOL.
See this image and copyright information in PMC

Comment in

Comment on

  • Structural basis of human PCNA sliding on DNA.
    De March M, Merino N, Barrera-Vilarmau S, Crehuet R, Onesti S, Blanco FJ, De Biasio A. De March M, et al. Nat Commun. 2017 Jan 10;8:13935. doi: 10.1038/ncomms13935. Nat Commun. 2017. PMID: 28071730 Free PMC article.

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