5u30: Difference between revisions

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 ==Crystal structure of AacC2c1-sgRNA-extended target DNA ternary complex==
-<StructureSection load='5u30' size='340' side='right' caption='[[5u30]], [[Resolution|resolution]] 2.92&Aring;' scene=''>
+<StructureSection load='5u30' size='340' side='right'caption='[[5u30]], [[Resolution|resolution]] 2.92&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5u30]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Aliag Aliag]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U30 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U30 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5u30]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alicyclobacillus_acidoterrestris Alicyclobacillus acidoterrestris], [https://en.wikipedia.org/wiki/Alicyclobacillus_acidoterrestris_ATCC_49025 Alicyclobacillus acidoterrestris ATCC 49025] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U30 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.92&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5u31|5u31]], [[5u33|5u33]], [[5u34|5u34]]</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=5u30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u30 OCA], [https://pdbe.org/5u30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u30 RCSB], [https://www.ebi.ac.uk/pdbsum/5u30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u30 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">c2c1, N007_06525 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1356854 ALIAG])</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=5u30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u30 OCA], [http://pdbe.org/5u30 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u30 RCSB], [http://www.ebi.ac.uk/pdbsum/5u30 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u30 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/C2C1_ALIAG C2C1_ALIAG]] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein (By similarity). The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA (By similarity). C2c1-crRNA-tracrRNA endonucleolytically cleaves dsDNA target complementary to the spacer; C2c1 is inactive in the absence of crRNA homologous to the target and tracrRNA (PubMed:26593719). C2c1 recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif) to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs (PubMed:26593719). PAM recognition is also required for catalytic activity. Cuts target DNA when C2c1, crRNA and tracrRNA are mixed (PubMed:26593719).[UniProtKB:A0Q5Y3]<ref>PMID:26593719</ref>
+[https://www.uniprot.org/uniprot/CS12B_ALIAG CS12B_ALIAG] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein (By similarity). The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA (By similarity). Protein-crRNA-tracrRNA endonucleolytically cleave dsDNA target complementary to the spacer; protein is inactive in the absence of crRNA homologous to the target and tracrRNA (PubMed:26593719). Recognizes a short motif in the CRISPR repeat sequences (the 5' PAM or protospacer adjacent motif, TTN in this organism) to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs (PubMed:26593719). PAM recognition is also required for catalytic activity. Cleavage results in staggered 6-8 base 5'-overhangs 14-17 and 23-24 bases downstream of the PAM (protospacer adjacent motif) on the non-target and target strands respectively (PubMed:27984729, PubMed:27989439). Both target and non-target strand DNA are probably independently cleaved in the same active site (PubMed:27984729).[UniProtKB:A0Q5Y3]<ref>PMID:26593719</ref> <ref>PMID:27984729</ref> <ref>PMID:27989439</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 5u30" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Aliag]]
+[[Category: Alicyclobacillus acidoterrestris]]
-[[Category: Gao, P]]
+[[Category: Alicyclobacillus acidoterrestris ATCC 49025]]
-[[Category: Patel, D J]]
+[[Category: Homo sapiens]]
-[[Category: Rajashankar, K R]]
+[[Category: Large Structures]]
-[[Category: Yang, H]]
+[[Category: Gao P]]
-[[Category: Hydrolase-dna complex]]
+[[Category: Patel DJ]]
-[[Category: Type v crispr-cas endonculease: c2c1: structure: binary complex with sgrna: ternary complex with added dna: ruvc catalytic pocket: sequence-specific pam recognition: genome editing tool]]
+[[Category: Rajashankar KR]]
+[[Category: Yang H]]