Talk:CRISPR-Cas9 Part II
From Proteopedia
List of figures: CRISPR-Cas9_Part_II
--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
