6E9F

EsCas13d-crRNA-target RNA ternary complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d.

Zhang, C.Konermann, S.Brideau, N.J.Lotfy, P.Wu, X.Novick, S.J.Strutzenberg, T.Griffin, P.R.Hsu, P.D.Lyumkis, D.

(2018) Cell 175: 212-223.e17

  • DOI: 10.1016/j.cell.2018.09.001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • CRISPR-Cas endonucleases directed against foreign nucleic acids mediate prokaryotic adaptive immunity and have been tailored for broad genetic engineering applications. Type VI-D CRISPR systems contain the smallest known family of single effector Cas ...

    CRISPR-Cas endonucleases directed against foreign nucleic acids mediate prokaryotic adaptive immunity and have been tailored for broad genetic engineering applications. Type VI-D CRISPR systems contain the smallest known family of single effector Cas enzymes, and their signature Cas13d ribonuclease employs guide RNAs to cleave matching target RNAs. To understand the molecular basis for Cas13d function and explain its compact molecular architecture, we resolved cryoelectron microscopy structures of Cas13d-guide RNA binary complex and Cas13d-guide-target RNA ternary complex to 3.4 and 3.3 Å resolution, respectively. Furthermore, a 6.5 Å reconstruction of apo Cas13d combined with hydrogen-deuterium exchange revealed conformational dynamics that have implications for RNA scanning. These structures, together with biochemical and cellular characterization, provide insights into its RNA-guided, RNA-targeting mechanism and delineate a blueprint for the rational design of improved transcriptome engineering technologies.


    Organizational Affiliation

    Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: dlyumkis@salk.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EsCas13dA954[Eubacterium] siraeum DSM 15702Mutation(s): 4 
Gene Names: EUBSIR_02687
Find proteins for B0MS50 ([Eubacterium] siraeum DSM 15702)
Explore B0MS50 
Go to UniProtKB:  B0MS50
Protein Feature View
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  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
crRNA (52-MER)B52bacterium

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
RNA (27-MER)C27bacterium
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-01 
  • Released Date: 2018-10-03 
  • Deposition Author(s): Zhang, C., Lyumkis, D.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesDP5 OD021396
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesU54GM103368

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Data collection
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence