Supplementary Materials

Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

David W. Taylor, Yifan Zhu, Raymond H. J. Staals, Jack E. Kornfeld, Akeo Shinkai, John van der Oost, Eva Nogales, Jennifer A. Doudna

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S3
  • Table S1
  • Captions for Movies S1 to S3
  • References (2329)

Images, Video, and Other Other Media

Movie S1
Superposition of intact and smaller apo-Cmr complexes. This movie shows the superposition of the top three Cm4 backbone subunits of the two species of apo-Cmr complex after alignment of the Cmr1¬–Cmr6 head. The smaller apo-Cmr complex subunits are removed and then added back sequentially from the bottom to the top of the complex to more clearly show the superposition.
Movie S2
Conformational rearrangements of Cmr upon target ssRNA recognition. This movie shows a morph between the apo-Cmr and Cmr bound to target ssRNA. First, apo-Cmr is shown with the crRNA in dark blue. Next, to emphasize the conformational rearrangements required for formation of a wider channel to accommodate target RNA, the crRNA is hidden, and the subunits are morphed from their apo- to target-bound state. Once in the target-bound state the crRNA:target RNA density is shown in blue. The movie then repeats in reverse (from target-bound to apo state). The morph was generated using the morph map function in UCSF Chimera. The two maps were aligned as in Fig. 1C, then morph maps were generated for each individual subunit (except Cmr4) to elucidate conformational changes upon target RNA binding. The movie and the next were generated using UCSF Chimera.
Movie S3
Architecture of the ssRNA target-bound Cmr. This movie shows 360° rotations of the target-bound Cmr complex with and without homology models docked into the complex. First, the four Cmr4 subunits; second, Cmr3 and Cmr6 are shown; third, the three Cmr5 subunits are added; fourth, the crRNA:target RNA duplex is shown; and fifth, the Cmr1 and Cmr2 subunits are added to show the architecture of the entire complex. The homology model for Cmr4 is docked as in Fig. 2B along with the crystal structures for Cmr2 (PDB 3UNG) (27), Cmr3 (PDB 4H4K) (28), and Cmr5 (PDB 2ZOP) (29).
Correction (3 April 2015): In the section �Docking and Homology Modeling� of Materials and Methods, the PDB ID of the crystal structure of PfCmr4 has been corrected.
The original version is accessible here.