This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5u30

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 19:25, 15 November 2017

Crystal structure of AacC2c1-sgRNA-extended target DNA ternary complex

Structural highlights

5u30 is a 4 chain structure with sequence from Aliag. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	5u31, 5u33, 5u34
Gene:	c2c1, N007_06525 (ALIAG)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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]^[1]

Publication Abstract from PubMed

C2c1 is a newly identified guide RNA-mediated type V-B CRISPR-Cas endonuclease that site-specifically targets and cleaves both strands of target DNA. We have determined crystal structures of Alicyclobacillus acidoterrestris C2c1 (AacC2c1) bound to sgRNA as a binary complex and to target DNAs as ternary complexes, thereby capturing catalytically competent conformations of AacC2c1 with both target and non-target DNA strands independently positioned within a single RuvC catalytic pocket. Moreover, C2c1-mediated cleavage results in a staggered seven-nucleotide break of target DNA. crRNA adopts a pre-ordered five-nucleotide A-form seed sequence in the binary complex, with release of an inserted tryptophan, facilitating zippering up of 20-bp guide RNA:target DNA heteroduplex on ternary complex formation. Notably, the PAM-interacting cleft adopts a "locked" conformation on ternary complex formation. Structural comparison of C2c1 ternary complexes with their Cas9 and Cpf1 counterparts highlights the diverse mechanisms adopted by these distinct CRISPR-Cas systems, thereby broadening and enhancing their applicability as genome editing tools.

PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease.,Yang H, Gao P, Rajashankar KR, Patel DJ Cell. 2016 Dec 15;167(7):1814-1828.e12. doi: 10.1016/j.cell.2016.11.053. PMID:27984729^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. Mol Cell. 2015 Nov 5;60(3):385-97. doi: 10.1016/j.molcel.2015.10.008. Epub 2015, Oct 22. PMID:26593719 doi:http://dx.doi.org/10.1016/j.molcel.2015.10.008
↑ Yang H, Gao P, Rajashankar KR, Patel DJ. PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease. Cell. 2016 Dec 15;167(7):1814-1828.e12. doi: 10.1016/j.cell.2016.11.053. PMID:27984729 doi:http://dx.doi.org/10.1016/j.cell.2016.11.053

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5u30"

@@ Line 3: / Line 3: @@
 <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. 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 [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>
 </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>
 <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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5u31|5u31]], [[5u33|5u33]], [[5u34|5u34]]</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>
@@ Line 24: / Line 25: @@
 __TOC__
 </StructureSection>
+[[Category: Aliag]]
 [[Category: Gao, P]]
 [[Category: Patel, D J]]

5u30

From Proteopedia

Revision as of 19:25, 15 November 2017

Crystal structure of AacC2c1-sgRNA-extended target DNA ternary complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox