5wqe

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with single-guide RNA at 3.1 Angstrom resolution

Structural highlights

5wqe is a 2 chain structure with sequence from Alicyclobacillus acidoterrestris ATCC 49025. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.126Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]^[1] ^[2] ^[3]

Publication Abstract from PubMed

C2c1 is a type V-B CRISPR-Cas system dual-RNA-guided DNA endonuclease. Here, we report the crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with a chimeric single-molecule guide RNA (sgRNA). AacC2c1 exhibits a bi-lobed architecture consisting of a REC and NUC lobe. The sgRNA scaffold forms a tetra-helical structure, distinct from previous predictions. The crRNA is located in the central channel of C2c1, and the tracrRNA resides in an external surface groove. Although AacC2c1 lacks a PAM-interacting domain, our analysis revealed that the PAM duplex has a similar binding position found in Cpf1. Importantly, C2c1-sgRNA system is highly sensitive to single-nucleotide mismatches between guide RNA and target DNA. The resulting reduction in off-target cleavage renders C2c1 a valuable addition to the current arsenal of genome-editing tools. Together, our findings indicate that sgRNA assembly is achieved through a mechanism distinct from that reported previously for Cas9 or Cpf1 endonucleases.

C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism.,Liu L, Chen P, Wang M, Li X, Wang J, Yin M, Wang Y Mol Cell. 2017 Jan 19;65(2):310-322. doi: 10.1016/j.molcel.2016.11.040. Epub 2016, Dec 15. PMID:27989439^[4]

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
↑ Liu L, Chen P, Wang M, Li X, Wang J, Yin M, Wang Y. C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism. Mol Cell. 2017 Jan 19;65(2):310-322. doi: 10.1016/j.molcel.2016.11.040. Epub 2016, Dec 15. PMID:27989439 doi:http://dx.doi.org/10.1016/j.molcel.2016.11.040
↑ Liu L, Chen P, Wang M, Li X, Wang J, Yin M, Wang Y. C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism. Mol Cell. 2017 Jan 19;65(2):310-322. doi: 10.1016/j.molcel.2016.11.040. Epub 2016, Dec 15. PMID:27989439 doi:http://dx.doi.org/10.1016/j.molcel.2016.11.040

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Alicyclobacillus acidoterrestris ATCC 49025 | Large Structures | Liu L | Wang YL

@@ Line 3: / Line 3: @@
 <StructureSection load='5wqe' size='340' side='right'caption='[[5wqe]], [[Resolution|resolution]] 3.13&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5wqe]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5WQE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5wqe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Alicyclobacillus_acidoterrestris_ATCC_49025 Alicyclobacillus acidoterrestris ATCC 49025]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WQE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WQE FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.126&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5wqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqe OCA], [http://pdbe.org/5wqe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wqe RCSB], [http://www.ebi.ac.uk/pdbsum/5wqe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqe ProSAT]</span></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></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=5wqe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wqe OCA], [https://pdbe.org/5wqe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wqe RCSB], [https://www.ebi.ac.uk/pdbsum/5wqe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wqe 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 26: / Line 27: @@
 __TOC__
 </StructureSection>
+[[Category: Alicyclobacillus acidoterrestris ATCC 49025]]
 [[Category: Large Structures]]
-[[Category: Liu, L]]
+[[Category: Liu L]]
-[[Category: Wang, Y L]]
+[[Category: Wang YL]]
-[[Category: Crispr-cas endonuclease]]
-[[Category: Nuclease lobe]]
-[[Category: Recognition lobe]]
-[[Category: Rna binding protein]]

5wqe

From Proteopedia

Current revision

Crystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with single-guide RNA at 3.1 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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