5b43: Difference between revisions

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 ==Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA==
-<StructureSection load='5b43' size='340' side='right' caption='[[5b43]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5b43' size='340' side='right'caption='[[5b43]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5b43]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B43 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B43 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5b43]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidaminococcus Acidaminococcus] and [https://en.wikipedia.org/wiki/Acidaminococcus_sp._BV3L6 Acidaminococcus sp. BV3L6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B43 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B43 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b43 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b43 OCA], [http://pdbe.org/5b43 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b43 RCSB], [http://www.ebi.ac.uk/pdbsum/5b43 PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5b43 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b43 OCA], [https://pdbe.org/5b43 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b43 RCSB], [https://www.ebi.ac.uk/pdbsum/5b43 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b43 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CPF1_ACISB CPF1_ACISB]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Has dsDNA endonuclease activity, results in a 4-base 5' overhang 19 and 22 bases downstream of the PAM on the non-targeted and targeted strand respectively (PubMed:26422227). In this CRISPR system correct processing of pre-crRNA requires only this protein and the CRISPR locus (By similarity).[UniProtKB:A0Q7Q2]<ref>PMID:26422227</ref>
+[https://www.uniprot.org/uniprot/CS12A_ACISB CS12A_ACISB] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif, TTTN in this organism) to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs (PubMed:26422227). Has dsDNA endonuclease activity, results in staggered 4-base 5' overhangs 19 and 22 bases downstream of the PAM on the non-targeted and targeted strand respectively (PubMed:26422227). Non-target strand cleavage by the RuvC domain is probably a prerequisite of target strand cleavage by the Nuc domain (PubMed:27114038). In this CRISPR system correct processing of pre-crRNA requires only this protein and the CRISPR locus (By similarity).[UniProtKB:A0Q7Q2]<ref>PMID:26422227</ref> <ref>PMID:27114038</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system that has been recently harnessed for genome editing. Here, we report the crystal structure of Acidaminococcus sp. Cpf1 (AsCpf1) in complex with the guide RNA and its target DNA at 2.8 A resolution. AsCpf1 adopts a bilobed architecture, with the RNA-DNA heteroduplex bound inside the central channel. The structural comparison of AsCpf1 with Cas9, a type II CRISPR-Cas nuclease, reveals both striking similarity and major differences, thereby explaining their distinct functionalities. AsCpf1 contains the RuvC domain and a putative novel nuclease domain, which are responsible for cleaving the non-target and target strands, respectively, and for jointly generating staggered DNA double-strand breaks. AsCpf1 recognizes the 5'-TTTN-3' protospacer adjacent motif by base and shape readout mechanisms. Our findings provide mechanistic insights into RNA-guided DNA cleavage by Cpf1 and establish a framework for rational engineering of the CRISPR-Cpf1 toolbox.
-Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA.,Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O Cell. 2016 May 5;165(4):949-62. doi: 10.1016/j.cell.2016.04.003. Epub 2016 Apr, 21. PMID:27114038<ref>PMID:27114038</ref>
+==See Also==
+*[[CRISPR type V|CRISPR type V]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+*[[CRISPR-Cas|CRISPR-Cas]]
-</div>
+*[[CRISPR-Cas Part II|CRISPR-Cas Part II]]
-<div class="pdbe-citations 5b43" style="background-color:#fffaf0;"></div>
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Hirano, H]]
+[[Category: Acidaminococcus]]
-[[Category: Ishitani, R]]
+[[Category: Acidaminococcus sp. BV3L6]]
-[[Category: Nakane, T]]
+[[Category: Large Structures]]
-[[Category: Nishimasu, H]]
+[[Category: Hirano H]]
-[[Category: Nureki, O]]
+[[Category: Ishitani R]]
-[[Category: Yamano, T]]
+[[Category: Nakane T]]
-[[Category: Hydrolase-rna-dna complex]]
+[[Category: Nishimasu H]]
-[[Category: Nuclease]]
+[[Category: Nureki O]]
+[[Category: Yamano T]]