Talk:CRISPR-Cas9

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Contents 1 List of figures: CRISPR-Cas9 1.1 Initial view 1.2 Domain organization of nuclease lobe of Cas9 from S. pyogenes 1.3 crRNA and tracrRNA can be joined end-to-end and transcribed as a single guide RNA (sgRNA) 1.4 Cas9-sgRNA-target DNA complex from Streptococcus pyogenes 1.5 Cas9-sgRNA-target DNA complex from Streptococcus pyogenes 1.6 Cas9-sgRNA-target DNA complex from Francisella tularensis 1.7 Cas9-sgRNA-target DNA complex from Staphylococcus aureus 1.8 optimal DNA target of the complex is determined by a Watson–Crick base pairing of a short ∼20-nt sequence within sgRNA (within the crRNA in wild-type) 1.9 few nucleotide long conserved motif recognized directly by Cas9 protein (protospacer adjacent motif, PAM) 1.10 few mismatches between guide sequence and target DNA can be tolerated 1.11 When Cas9 is in the apo state, its PAM-interacting cleft is largely disordered 1.12 Pre-target state of CAS9 with sgRNA 1.13 CAS9 with sgRNA and tagret DNA 1.14 Animation of these scenes 1.15 Cas9-sgRNA-dsDNA complex 1.16 sgRNA-dsDNA without protein is shown 1.17 Scissile phosphates 1.18 Cas9 interacts with both separated DNA strands 1.19 deactivated Cas9 (dCas9) 1.20 mutating two key residues within its nuclease domains 1.21 Domain organization of nuclease lobe of Cas9 from S. pyogenes 1.22 Cas9-sgRNA-target DNA complex from Streptococcus pyogenes 1.23 Cas9-sgRNA-target DNA complex from Streptococcus pyogenes 1.24 CAS9 with sgRNA and tagret DNA 1.25 Cas9-sgRNA-dsDNA complex 1.26 Jmol commands: buttons etc 1.27 Summary 1.27.1 coordinates used

List of figures: CRISPR-Cas9

--Karsten Theis 01:51, 20 July 2019 (UTC)

Initial view

script: https://proteopedia.org/wiki/scripts/74/742625/Cv3/13.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?14e7e6b27144899555581f95781095d3 (always reloads)

Domain organization of nuclease lobe of Cas9 from S. pyogenes

script: https://proteopedia.org/wiki/scripts/74/746096/Cv3/1.spt

coords: same as Initial view (always reloads)

crRNA and tracrRNA can be joined end-to-end and transcribed as a single guide RNA (sgRNA)

script: https://proteopedia.org/wiki/scripts/74/742625/Cv3/8.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?390674a1fe8f149d2a471a66257db804 (always reloads)

Cas9-sgRNA-target DNA complex from Streptococcus pyogenes

script: https://proteopedia.org/wiki/scripts/74/742625/Cv/42.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?24390165f6e745806f0ed99c67de2118 (always reloads)

Cas9-sgRNA-target DNA complex from Streptococcus pyogenes

script: https://proteopedia.org/wiki/scripts/74/742625/Cv2/12.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?9dbb58242e693852cd408648accf59ea (always reloads)

Cas9-sgRNA-target DNA complex from Francisella tularensis

script: https://proteopedia.org/wiki/scripts/74/742625/Cv2/13.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?0a7d3ac27b1d671cca434c9eff24c49c (always reloads)

Cas9-sgRNA-target DNA complex from Staphylococcus aureus

script: https://proteopedia.org/wiki/scripts/74/742625/Cv3/2.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?2ccede112780a94592edf96642f32d01 (always reloads)

optimal DNA target of the complex is determined by a Watson–Crick base pairing of a short ∼20-nt sequence within sgRNA (within the crRNA in wild-type)

script: https://proteopedia.org/wiki/scripts/74/742625/Cv3/4.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?e44061e874ac35d8806b45eaf9f9ebaf (always reloads)

few nucleotide long conserved motif recognized directly by Cas9 protein (protospacer adjacent motif, PAM)

script: https://proteopedia.org/wiki/scripts/74/742625/Cv3/10.spt

coords: same as optimal DNA target of the complex is determined by a Watson–Crick base pairing of a short ∼20-nt sequence within sgRNA (within the crRNA in wild-type) (always reloads)

few mismatches between guide sequence and target DNA can be tolerated

script: https://proteopedia.org/wiki/scripts/74/742625/Cv/44.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?3d79d333a058bb5bd2af9650e145ebe1 (always reloads)

When Cas9 is in the apo state, its PAM-interacting cleft is largely disordered

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/3.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?ce8514cc5aaf7818a31c1779fc0adf71 (always reloads)

Pre-target state of CAS9 with sgRNA

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/4.spt

coords: same as When Cas9 is in the apo state, its PAM-interacting cleft is largely disordered (always reloads)

CAS9 with sgRNA and tagret DNA

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/5.spt

coords: same as When Cas9 is in the apo state, its PAM-interacting cleft is largely disordered (always reloads)

Animation of these scenes

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/7.spt

coords: same as When Cas9 is in the apo state, its PAM-interacting cleft is largely disordered (always reloads)

Cas9-sgRNA-dsDNA complex

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/11.spt

coords: https://proteopedia.org/cgi-bin/getfrozenstructure?e9eee6ce3083b7b447d2efbbf956be6c (always reloads)

sgRNA-dsDNA without protein is shown

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/12.spt

coords: same as Cas9-sgRNA-dsDNA complex (always reloads)

Scissile phosphates

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/14.spt

coords: same as Cas9-sgRNA-dsDNA complex (always reloads)

Cas9 interacts with both separated DNA strands

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/15.spt

coords: same as Cas9-sgRNA-dsDNA complex (always reloads)

deactivated Cas9 (dCas9)

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/8.spt

coords: same as crRNA and tracrRNA can be joined end-to-end and transcribed as a single guide RNA (sgRNA) (always reloads)

mutating two key residues within its nuclease domains

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/9.spt

coords: same as crRNA and tracrRNA can be joined end-to-end and transcribed as a single guide RNA (sgRNA) (always reloads)

Domain organization of nuclease lobe of Cas9 from S. pyogenes

script: https://proteopedia.org/wiki/scripts/74/746096/Cv3/1.spt

coords: same as Initial view (always reloads)

Cas9-sgRNA-target DNA complex from Streptococcus pyogenes

script: https://proteopedia.org/wiki/scripts/74/742625/Cv/42.spt

coords: same as Cas9-sgRNA-target DNA complex from Streptococcus pyogenes (always reloads)

Cas9-sgRNA-target DNA complex from Streptococcus pyogenes

script: https://proteopedia.org/wiki/scripts/74/742625/Cv2/12.spt

coords: same as Cas9-sgRNA-target DNA complex from Streptococcus pyogenes (always reloads)

CAS9 with sgRNA and tagret DNA

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/5.spt

coords: same as When Cas9 is in the apo state, its PAM-interacting cleft is largely disordered (always reloads)

Cas9-sgRNA-dsDNA complex

script: https://proteopedia.org/wiki/scripts/74/742625/Cv4/11.spt

coords: same as Cas9-sgRNA-dsDNA complex (always reloads)

Jmol commands: buttons etc

Summary

Total of green links: 25

Total of Jmol buttons etc: 0

coordinates used

• /cgi-bin/getfrozenstructure?14e7e6b27144899555581f95781095d3
• /cgi-bin/getfrozenstructure?390674a1fe8f149d2a471a66257db804
• /cgi-bin/getfrozenstructure?24390165f6e745806f0ed99c67de2118
• /cgi-bin/getfrozenstructure?9dbb58242e693852cd408648accf59ea
• /cgi-bin/getfrozenstructure?0a7d3ac27b1d671cca434c9eff24c49c
• /cgi-bin/getfrozenstructure?2ccede112780a94592edf96642f32d01
• /cgi-bin/getfrozenstructure?e44061e874ac35d8806b45eaf9f9ebaf
• /cgi-bin/getfrozenstructure?3d79d333a058bb5bd2af9650e145ebe1
• /cgi-bin/getfrozenstructure?ce8514cc5aaf7818a31c1779fc0adf71
• /cgi-bin/getfrozenstructure?e9eee6ce3083b7b447d2efbbf956be6c