5cd4

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'''Unreleased structure'''
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==The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back==
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<StructureSection load='5cd4' size='340' side='right' caption='[[5cd4]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5cd4]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CD4 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene></td></tr>
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<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=5cd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cd4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5cd4 RCSB], [http://www.ebi.ac.uk/pdbsum/5cd4 PDBsum]</span></td></tr>
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</table>
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== Function ==
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[[http://www.uniprot.org/uniprot/CSE1_ECOLI CSE1_ECOLI]] 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).<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:22621933</ref> <ref>PMID:22521690</ref> A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, probably via interactions with CasA, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization. CasA is not required for formation of Cascade, but probably enhances binding to and subsequent recognition of both target dsDNA and ssDNA.<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:22621933</ref> <ref>PMID:22521690</ref> [[http://www.uniprot.org/uniprot/CAS6_ECOLI CAS6_ECOLI]] 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).<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> CasE is required to process the pre-crRNA into single repeat-spacer units, with an 8-nt 5'-repeat DNA tag that may help other proteins recognize the crRNA. This subunit alone will cleave pre-crRNA, as will CasCDE or CasCE; cleavage does not require divalent metals or ATP. CasCDE alone is also able to form R-loops. Partially inhibits the cleavage of Holliday junctions by YgbT (Cas1). Yields a 5'-hydroxy group and a 2',3'-cyclic phosphate terminus.<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization.<ref>PMID:18703739</ref> <ref>PMID:21219465</ref> <ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> [[http://www.uniprot.org/uniprot/CAS5_ECOLI CAS5_ECOLI]] 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).<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization. CasCDE alone is also able to form R-loops.<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> [[http://www.uniprot.org/uniprot/CASC_ECOLI CASC_ECOLI]] 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).<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization. CasCDE alone is also able to form R-loops.<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> <ref>PMID:21699496</ref> [[http://www.uniprot.org/uniprot/CSE2_ECOLI CSE2_ECOLI]] 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).<ref>PMID:21255106</ref> <ref>PMID:21460843</ref> A component of Cascade, which participates in CRISPR interference, the third stage of CRISPR immunity. Cascade binds both crRNA and in a sequence-specific manner negatively supercoiled dsDNA target. This leads to the formation of an R-loop in which the crRNA binds the target DNA, displacing the noncomplementary strand. Cas3 is recruited to Cascade, nicks target DNA and then unwinds and cleaves the target, leading to DNA degradation and invader neutralization.<ref>PMID:21255106</ref> <ref>PMID:21460843</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli, short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 A x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro. Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.
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The entry 5cd4 is ON HOLD
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Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli.,van Erp PB, Jackson RN, Carter J, Golden SM, Bailey S, Wiedenheft B Nucleic Acids Res. 2015 Aug 3. pii: gkv793. PMID:26243775<ref>PMID:26243775</ref>
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Authors: Jackson, R.N., Golden, S.M., Carter, J., Wiedenheft, B.
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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Description:
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== References ==
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[[Category: Unreleased Structures]]
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<references/>
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[[Category: Golden, S.M]]
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__TOC__
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[[Category: Jackson, R.N]]
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</StructureSection>
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[[Category: Carter, J]]
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[[Category: Golden, S M]]
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[[Category: Jackson, R N]]
[[Category: Wiedenheft, B]]
[[Category: Wiedenheft, B]]
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[[Category: Carter, J]]
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[[Category: Adaptive immunity]]
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[[Category: Cascade]]
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[[Category: Crispr]]
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[[Category: Hydrolase-rna complex]]
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[[Category: Rna surveillance]]

Revision as of 13:24, 26 August 2015

The Type IE CRISPR Cascade complex from E. coli, with two assemblies in the asymmetric unit arranged back-to-back

5cd4, resolution 3.20Å

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