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Contributed by Charles C. Richardson, January 27, 2017 (sent for review December 7, 2016; reviewed by James M. Berger and Nicholas E. Dixon)
Article Figures & SI
Figures
- Fig. 1.
cryo-EM analysis and assembly of the replisome. (A) A fork-shaped DNA is formed by folding of ssDNA such that a stable tetra-loop is formed in the middle of the sequence flanked by a short double-helical region; two oligonucleotides are annealed to serve as primers. (B and C) Melting profiles of the tetra-loop DNA. Samples containing different concentrations of the fork-shaped DNA are represented by colored curved lines. Melting curves (B) and their first derivatives (C) show a biphasic transition with the melting temperatures (Tm) of 53 ± 2 °C. (D) Fluorescence anisotropy measurements of replisome formation. The replication complex assembled in the presence of gp4-E343Q is four times more stable than the complex assembled with wild-type gp4. Apparent binding constants are 0.2 ± 0.01 µM and 0.8 ± 0.05 µM, respectively. (E) A representative cryo-EM image. (Scale bar, 10 nm.) (F) The 2D class averages. (Scale bar, 10 nm.) (G) A calculated 3D map of the replisome. The initial model for the 3D calculation was generated using the atomic coordinates of the helicase domain of gp4 filtered to a resolution of 60 Å. (H) Fourier Schell Correlation (FSC). The resolution of 13.8 Å is based on the gold-standard FSC0.5 criterion. (I) Comparison of reprojections from the 3D structure with the 2D class averages. (Scale bar, 10 nm.)
- Fig. 2.
Architecture of the replisome. (A) The structure reveals the presence of the hexameric ring of DNA helicase (blue), five covalently linked DNA primase domains (orange), and two gp5/trx complexes. The polymerase domain (green) and the exonuclease domain (purple) of gp5 as well as thioredoxin (yellow) are indicated. The two molecules of DNA polymerase bind to gp4 in an asymmetric fashion, reflecting their roles in leading- and lagging-strand synthesis (gp5/trxlead and gp5/trxlag, respectively). (B) An asymmetric arrangement of RNA primases at the replisome.
- Fig. 3.
Intermolecular interactions at the replisome. (A) Interaction of gp5/trxlead and gp4. (B) The fingers of gp5/trxlead interact with the loop connecting α-helices H1 and H2 in the thumb domain. (C) Gp5/trxlead adopts a closed conformation of the polymerase active site, in which the thumb and fingers are rotated inward. (D) In contrast, the polymearse active site of gp5/trxlag adopts an open conformation. In this open conformation, the fingers rotate outward away from the thumb. (E) Interaction between gp5/trxlag and gp4. (F) Trx binds to a unique 76-amino-acid loop, TBD, inserted in the thumb subdomain of gp5/trxlag. (G) Binding of gp5/trxlead and gp5/trxlag. The specific interactions are described in the text.
- Fig. 4.
Architecture of the replication fork and a model for formation of the lagging-strand replication loop. (A) A model of the replication fork before formation of the replication loop on the lagging strand. (B) Polymerization of nucleotides by gp5/trxlag combined with the movement of ssDNA through the central cavity of gp4 accounts for formation of the replication loop on the lagging strand.
Data supplements
Supporting Information
- Download Supporting Information (PDF)
- Download Appendix (PDF)
- Download Movie_S01 (MP4) - The movie shows a cryo-EM structure of the replisome and fitted atomic coordinates of the replication protein.
Cryo-EM structure of the replisome
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- Biological Sciences
- Biophysics and Computational Biology
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