3X1L image
Deposition Date 2014-11-20
Release Date 2015-05-13
Last Version Date 2024-05-29
Entry Detail
PDB ID:
3X1L
Keywords:
RNA BINDING PROTEIN/RNA/DNA
Title:
Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog
Biological Source:
Source Organism:
Pyrococcus furiosus DSM 3638 (Taxon ID: 186497)
Archaeoglobus fulgidus DSM 4304 (Taxon ID: 224325)
Pyrococcus furiosus COM1 (Taxon ID: 1185654)
synthetic (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.10 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 1
3X1L validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CRISPR system Cmr subunit Cmr2
Gene (Uniprot):cmr2
Chain IDs:A
Chain Length:677
Number of Molecules:1
Biological Source:Pyrococcus furiosus DSM 3638
UniProt ID:Q8U1S6 Pfam ID:PF12469, PF20823, PF20822, PF22335, PF20824
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CRISPR system Cmr subunit Cmr3
Gene (Uniprot):cmr3
Chain IDs:B
Chain Length:322
Number of Molecules:1
Biological Source:Pyrococcus furiosus DSM 3638
UniProt ID:Q8U1S7 Pfam ID:PF09700
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cmr4
Gene (Uniprot):AF_1863
Chain IDs:C, D, E
Chain Length:357
Number of Molecules:3
Biological Source:Archaeoglobus fulgidus DSM 4304
UniProt ID:O28416 Pfam ID:PF03787
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CRISPR system Cmr subunit Cmr5
Gene (Uniprot):cmr5
Chain IDs:F, G
Chain Length:155
Number of Molecules:2
Biological Source:Archaeoglobus fulgidus DSM 4304
UniProt ID:O28417 Pfam ID:PF09701
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cmr6
Gene (Uniprot):AF_1861
Chain IDs:H
Chain Length:349
Number of Molecules:1
Biological Source:Archaeoglobus fulgidus DSM 4304
UniProt ID:O28418 Pfam ID:PF03787
Polymer Type:polyribonucleotide
Molecule:RNA (32-MER)
Chain IDs:I
Chain Length:39
Number of Molecules:1
Biological Source:Pyrococcus furiosus COM1
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3')
Chain IDs:J
Chain Length:31
Number of Molecules:1
Biological Source:synthetic
Ligand Molecules
MG
ZN
Primary Citation
Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog.
Mol.Cell 58 418 430 (2015)
PMID: 25921071 DOI: 10.1016/j.molcel.2015.03.018

Abstact

In prokaryotes, Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs), together with CRISPR-associated (Cas) proteins, capture and degrade invading genetic materials. In the type III-B CRISPR-Cas system, six Cas proteins (Cmr1-Cmr6) and a crRNA form an RNA silencing Cmr complex. Here we report the 2.1 Å crystal structure of the Cmr1-deficient, functional Cmr complex bound to single-stranded DNA, a substrate analog complementary to the crRNA guide. Cmr3 recognizes the crRNA 5' tag and defines the start position of the guide-target duplex, using its idiosyncratic loops. The β-hairpins of three Cmr4 subunits intercalate within the duplex, causing nucleotide displacements with 6 nt intervals, and thus periodically placing the scissile bonds near the crucial aspartate of Cmr4. The structure reveals the mechanism for specifying the periodic target cleavage sites from the crRNA 5' tag and provides insights into the assembly of the type III interference machineries and the evolution of the Cmr and Cascade complexes.

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Primary Citation of related structures
3X1L