3X1L

Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Literature

Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog

Osawa, T.Inanaga, H.Sato, C.Numata, T.

(2015) Mol Cell 

  • DOI: 10.1016/j.molcel.2015.03.018
  • Primary Citation of Related Structures:  
    3X1L

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan. Electronic address: t-numata@aist.go.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cmr subunit Cmr2 A677Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: cmr2PF1129
Find proteins for Q8U1S6 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U1S6
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cmr subunit Cmr3 B322Pyrococcus furiosus DSM 3638Mutation(s): 0 
Gene Names: cmr3PF1128
Find proteins for Q8U1S7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
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Go to UniProtKB:  Q8U1S7
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cmr4 CDE357Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF_1863
Find proteins for O28416 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
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Go to UniProtKB:  O28416
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR system Cmr subunit Cmr5 FG155Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF_1861cmr5AF_1862
Find proteins for O28417 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
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Go to UniProtKB:  O28417
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cmr6 H349Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: AF_1861
Find proteins for O28418 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
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Go to UniProtKB:  O28418
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsLengthOrganismImage
RNA (32-MER)I39Pyrococcus furiosus COM1
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Entity ID: 7
MoleculeChainsLengthOrganismImage
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')J31synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.489α = 90.32
b = 76.215β = 104.83
c = 139.188γ = 118.58
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-11-20 
  • Released Date: 2015-05-13 
  • Deposition Author(s): Osawa, T., Numata, T.

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Structure summary