4rdp

From Proteopedia

(Difference between revisions)

Revision as of 06:50, 2 March 2023

Crystal structure of Cmr4

Structural highlights

4rdp is a 2 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CMR4_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.^[1]

Publication Abstract from PubMed

The Cmr complex is the multisubunit effector complex of the type III-B clustered regularly interspaced short palindromic repeats (CRISPR)-Cas immune system. The Cmr complex recognizes a target RNA through base pairing with the integral CRISPR RNA (crRNA) and cleaves the target at multiple regularly spaced locations within the complementary region. To understand the molecular basis of the function of this complex, we have assembled information from electron microscopic and X-ray crystallographic structural studies and mutagenesis of a complete Pyrococcus furiosus Cmr complex. Our findings reveal that four helically packed Cmr4 subunits, which make up the backbone of the Cmr complex, act as a platform to support crRNA binding and target RNA cleavage. Interestingly, we found a hook-like structural feature associated with Cmr4 that is likely the site of target RNA binding and cleavage. Our results also elucidate analogies in the mechanisms of crRNA and target molecule binding by the distinct Cmr type III-A and Cascade type I-E complexes.

Essential Structural and Functional Roles of the Cmr4 Subunit in RNA Cleavage by the Cmr CRISPR-Cas Complex.,Ramia NF, Spilman M, Tang L, Shao Y, Elmore J, Hale C, Cocozaki A, Bhattacharya N, Terns RM, Terns MP, Li H, Stagg SM Cell Rep. 2014 Dec 11;9(5):1610-7. doi: 10.1016/j.celrep.2014.11.007. Epub 2014, Dec 4. PMID:25482566^[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
↑ Ramia NF, Spilman M, Tang L, Shao Y, Elmore J, Hale C, Cocozaki A, Bhattacharya N, Terns RM, Terns MP, Li H, Stagg SM. Essential Structural and Functional Roles of the Cmr4 Subunit in RNA Cleavage by the Cmr CRISPR-Cas Complex. Cell Rep. 2014 Dec 11;9(5):1610-7. doi: 10.1016/j.celrep.2014.11.007. Epub 2014, Dec 4. PMID:25482566 doi:http://dx.doi.org/10.1016/j.celrep.2014.11.007

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/4rdp"

Categories: Large Structures | Pyrococcus furiosus | Li H | Shao Y | Tang L

@@ Line 3: / Line 3: @@
 <StructureSection load='4rdp' size='340' side='right'caption='[[4rdp]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rdp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RDP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rdp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RDP FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cmr4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
+</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=4rdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rdp OCA], [https://pdbe.org/4rdp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rdp RCSB], [https://www.ebi.ac.uk/pdbsum/4rdp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rdp ProSAT]</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=4rdp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rdp OCA], [http://pdbe.org/4rdp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rdp RCSB], [http://www.ebi.ac.uk/pdbsum/4rdp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rdp ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CMR4_PYRFU CMR4_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.<ref>PMID:19945378</ref>
+[https://www.uniprot.org/uniprot/CMR4_PYRFU CMR4_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.<ref>PMID:19945378</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43587]]
 [[Category: Large Structures]]
-[[Category: Li, H]]
+[[Category: Pyrococcus furiosus]]
-[[Category: Shao, Y]]
+[[Category: Li H]]
-[[Category: Tang, L]]
+[[Category: Shao Y]]
-[[Category: Ferredoxin-like fold]]
+[[Category: Tang L]]
-[[Category: Rna binding protein]]
-[[Category: Rrm]]

4rdp

From Proteopedia

Revision as of 06:50, 2 March 2023

Crystal structure of Cmr4

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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