Karsten Theis: New page: ==List of figures: CRISPR-Cas9_Part_II== --~~~~ ===Initial view=== script: https://proteopedia.org/wiki/scripts/79/795985/Cv/1.spt coords: https://proteopedia.org/cgi-bin/getfrozenstructu...

Karsten Theis — Sat, 20 Jul 2019 04:07:32 GMT

New page: ==List of figures: CRISPR-Cas9_Part_II== --~~~~ ===Initial view=== script: https://proteopedia.org/wiki/scripts/79/795985/Cv/1.spt coords: https://proteopedia.org/cgi-bin/getfrozenstructu...

New page

==List of figures: CRISPR-Cas9_Part_II==
--[[User:Karsten Theis|Karsten Theis]] 04:07, 20 July 2019 (UTC)
===Initial view===
script: https://proteopedia.org/wiki/scripts/79/795985/Cv/1.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9d62f8638c6affb57615762ffba03252

===crystal structure of full-length SaCas9===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv/48.spt

coords: same as Initial view

===bilobed architecture===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/1.spt

coords: same as Initial view

===two lobes are connected===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/2.spt

coords: same as Initial view

===NUC lobe consists of===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/3.spt

coords: same as Initial view

===PI domain===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/4.spt

coords: same as Initial view

===RuvC domain consists of===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/5.spt

coords: same as Initial view

===HNH domain===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/6.spt

coords: same as Initial view

===‘‘phosphate lock’’===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/7.spt

coords: same as Initial view

===quaternary complex structure of SaCas9 adopts a similar open conformation to form the central channel, which accommodates the guide:target heteroduplex===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/9.spt

coords: same as Initial view

===guide:target heteroduplex===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/11.spt

coords: same as Initial view

===PAM-containing duplex===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/12.spt

coords: same as Initial view

===repeat:anti-repeat duplex===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/13.spt

coords: same as Initial view

===Stem loop 1===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/16.spt

coords: same as Initial view

===guide:target heteroduplex is accommodated in the central channel===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/17.spt

coords: same as Initial view

===REC lobe (Thr238, Tyr239, Lys248, Tyr256, Arg314, Asn394, and Gln414)===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/20.spt

coords: same as Initial view

===by the bridge helix (Asn44, Arg48, Arg51, Arg55, Arg59, and Arg60) and the REC lobe (Arg116, Gly117, Arg165, Gly166, Asn169, Arg208, Arg209, and Tyr211)===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/23.spt

coords: same as Initial view

===repeat:anti-repeat duplex is recognized by the REC and WED domains, primarily through interactions between the protein and the sugar-phosphate backbone===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/32.spt

coords: same as Initial view

===internal loop is recognized by the WED domain===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/33.spt

coords: same as Initial view

===Tyr868===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/34.spt

coords: same as Initial view

===Lys870, Arg792, and Lys881===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/35.spt

coords: same as Initial view

===stem loop 1===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/39.spt

coords: same as Initial view

===Arg47, Arg54, Arg55, Arg58, and Arg59===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/40.spt

coords: same as Initial view

===Arg209, Gly216, and Ser219===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/41.spt

coords: same as Initial view

===2\===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/42.spt

coords: same as Initial view

===U64 is recognized by Arg209 and Glu213 via stacking and hydrogen-bonding interactions===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv6/43.spt

coords: same as Initial view

===N6, N7, and 2\===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv7/3.spt

coords: same as Initial view

===Lys57 interacts with the backbone phosphate group between C54 and A55, and the side chain of Leu783 forms hydrophobic contacts with the nucleobases of A55 and A56===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv7/4.spt

coords: same as Initial view

===linker region electrostatically interacts with the RuvC domain (Arg452, Lys459, and Arg774) and the phosphate lock loop (Arg781)===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv7/5.spt

coords: same as Initial view

===G70 stacks with the side chain of Arg47===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv7/6.spt

coords: same as Initial view

===5\===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv8/3.spt

coords: same as Initial view

===5\===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv9/3.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?2ccede112780a94592edf96642f32d01

===N7 atoms of dA4* and dA5* form direct and water-mediated hydrogen bonds with Asn985 and Asn985/Asn986/Arg991===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv8/4.spt

coords: same as Initial view

===N7 atoms of dG4* and dG5* form direct and water-mediated hydrogen bonds with Asn985 and Asn985/Asn986/Arg991===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv9/4.spt

coords: same as 5\

===the phosphate backbone of the PAM duplex is recognized from the minor groove side by the WED domain (Tyr789, Tyr882, Lys886, Ans888, Ala889, and Leu909)===
script: https://proteopedia.org/wiki/scripts/74/742625/Cv8/6.spt

coords: same as Initial view

===hydrogen bonds with the main-chain amide groups of Asp786 and Thr787 and the side chain of Thr787 in the phosphate lock loop===
script: https://proteopedia.org/wiki/scripts/79/795985/Cv9/1.spt

coords: same as 5\

===Asp10, Glu477, His701, and Asp704===
script: https://proteopedia.org/wiki/scripts/79/795985/Cv6/1.spt

coords: same as Initial view

===Asp556, His557, and Asn580===
script: https://proteopedia.org/wiki/scripts/79/795985/Cv6/2.spt

coords: same as Initial view

===RuvC and HNH domains are connected by α-helical linkers, L1 and L2===
script: https://proteopedia.org/wiki/scripts/79/795985/Cv6/3.spt

coords: same as Initial view

===Jmol commands: buttons etc===
===Summary===
Total of green links: 39

Total of Jmol buttons etc: 0
====coordinates used====
*5CZZ: https://proteopedia.org/cgi-bin/getfrozenstructure?9d62f8638c6affb57615762ffba03252
*5AXW: https://proteopedia.org/cgi-bin/getfrozenstructure?2ccede112780a94592edf96642f32d01

Talk:CRISPR-Cas9 Part II - Revision history

Karsten Theis: New page: ==List of figures: CRISPR-Cas9_Part_II== --~~~~ ===Initial view=== script: https://proteopedia.org/wiki/scripts/79/795985/Cv/1.spt coords: https://proteopedia.org/cgi-bin/getfrozenstructu...