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.

4h4k

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 18:03, 10 May 2016

Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex

Structural highlights

4h4k is a 2 chain structure with sequence from Pyrfu. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	cmr3, PF1128 (PYRFU), cmr2, PF1129 (PYRFU)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[CMR3_PYRFU] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. [CMR2_PYRFU] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.^[1]

Publication Abstract from PubMed

The Cmr complex is an RNA-guided effector complex that cleaves invader RNA in the prokaryotic immune response mediated by the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)-Cas system. Here, we report the crystal structure of a Cmr subcomplex containing Cmr2 (Cas10) and Cmr3 subunits at 2.8 A resolution. The structure revealed a dual ferredoxin fold and glycine-rich loops characteristic of previously known repeat-associated mysterious proteins and two unique insertion elements in Cmr3 that mediate its interaction with Cmr2. Surprisingly, while mutation of both insertion elements significantly weakened Cmr3-Cmr2 interaction, they exhibit differential effects on Cmr-mediated RNA cleavage by the Cmr complex, suggesting stabilization of Cmr2-Cmr3 interactions by other subunits. Further mutational analysis of the two conserved (but non-Cmr2-binding) glycine-rich loops of Cmr3 identified a region that is likely involved in assembly or the RNA cleavage function of the Cmr complex.

Structure of the Cmr2-Cmr3 Subcomplex of the Cmr RNA Silencing Complex.,Shao Y, Cocozaki AI, Ramia NF, Terns RM, Terns MP, Li H Structure. 2013 Feb 5. pii: S0969-2126(13)00004-X. doi:, 10.1016/j.str.2013.01.002. PMID:23395183^[2]

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

References

↑ Hale CR, Zhao P, Olson S, Duff MO, Graveley BR, Wells L, Terns RM, Terns MP. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell. 2009 Nov 25;139(5):945-56. doi: 10.1016/j.cell.2009.07.040. PMID:19945378 doi:10.1016/j.cell.2009.07.040
↑ Shao Y, Cocozaki AI, Ramia NF, Terns RM, Terns MP, Li H. Structure of the Cmr2-Cmr3 Subcomplex of the Cmr RNA Silencing Complex. Structure. 2013 Feb 5. pii: S0969-2126(13)00004-X. doi:, 10.1016/j.str.2013.01.002. PMID:23395183 doi:http://dx.doi.org/10.1016/j.str.2013.01.002

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/4h4k"

@@ Line 1: / Line 1: @@
 ==Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex==
 <StructureSection load='4h4k' size='340' side='right' caption='[[4h4k]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4h4k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus_dsm_3638 Pyrococcus furiosus dsm 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H4K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4h4k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H4K FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cmr3, PF1128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638]), cmr2, PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cmr3, PF1128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), cmr2, PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4h4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4k OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h4k RCSB], [http://www.ebi.ac.uk/pdbsum/4h4k PDBsum]</span></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=4h4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h4k OCA], [http://pdbe.org/4h4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h4k RCSB], [http://www.ebi.ac.uk/pdbsum/4h4k PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4h4k" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 24: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus furiosus dsm 3638]]
+[[Category: Pyrfu]]
 [[Category: Cocozaki, A I]]
 [[Category: Li, H]]

4h4k

From Proteopedia

Revision as of 18:03, 10 May 2016

Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox