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6iv9

From Proteopedia

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Current revision

the Cas13d binary complex

Structural highlights

6iv9 is a 2 chain structure with sequence from Uncultured Ruminococcus sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.86Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A1C5SD84_9FIRM

Publication Abstract from PubMed

Cas13d, the type VI-D CRISPR-Cas effector, is an RNA-guided ribonuclease that has been repurposed to edit RNA in a programmable manner. Here we report the detailed structural and functional analysis of the uncultured Ruminococcus sp. Cas13d (UrCas13d)-crRNA complex. Two hydrated Mg(2+) ions aid in stabilizing the conformation of the crRNA repeat region. Sequestration of divalent metal ions does not alter pre-crRNA processing, but abolishes target cleavage by UrCas13d. Notably, the pre-crRNA processing is executed by the HEPN-2 domain. Furthermore, both the structure and sequence of the nucleotides U(-8)-C(-1) within the repeat region are indispensable for target cleavage, and are specifically recognized by UrCas13d. Moreover, correct base pairings within two separate spacer regions (an internal and a 3'-end region) are essential for target cleavage. These findings provide a framework for the development of Cas13d into a tool for a wide range of applications.

Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d.,Zhang B, Ye Y, Ye W, Perculija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S Nat Commun. 2019 Jun 11;10(1):2544. doi: 10.1038/s41467-019-10507-3. PMID:31186424^[1]

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

References

↑ Zhang B, Ye Y, Ye W, Perculija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S. Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Nat Commun. 2019 Jun 11;10(1):2544. doi: 10.1038/s41467-019-10507-3. PMID:31186424 doi:http://dx.doi.org/10.1038/s41467-019-10507-3

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/6iv9"

@@ Line 3: / Line 3: @@
 <StructureSection load='6iv9' size='340' side='right'caption='[[6iv9]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6iv9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IV9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6iv9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_Ruminococcus_sp. Uncultured Ruminococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IV9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.86&#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=6iv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iv9 OCA], [http://pdbe.org/6iv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iv9 RCSB], [http://www.ebi.ac.uk/pdbsum/6iv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iv9 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6iv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iv9 OCA], [https://pdbe.org/6iv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iv9 RCSB], [https://www.ebi.ac.uk/pdbsum/6iv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iv9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A1C5SD84_9FIRM A0A1C5SD84_9FIRM]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: OuYang, S Y]]
+[[Category: Uncultured Ruminococcus sp]]
-[[Category: Ye, W W]]
+[[Category: OuYang SY]]
-[[Category: Ye, Y M]]
+[[Category: Ye WW]]
-[[Category: Zhang, B]]
+[[Category: Ye YM]]
-[[Category: Binary complex]]
+[[Category: Zhang B]]
-[[Category: Cas13d]]
-[[Category: Crispr]]
-[[Category: Crrna]]
-[[Category: Rna binding protein-rna complex]]

6iv9

From Proteopedia

Current revision

the Cas13d binary complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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