8D2L

Structure of Acidothermus cellulolyticus Cas9 ternary complex (Cleavage Intermediate 1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Coupled catalytic states and the role of metal coordination in Cas9.

Das, A.Rai, J.Roth, M.O.Shu, Y.Medina, M.L.Barakat, M.R.Li, H.

(2023) Nat Catal 6: 969-977

  • DOI: https://doi.org/10.1038/s41929-023-01031-1
  • Primary Citation of Related Structures:  
    8D2K, 8D2L, 8D2N, 8D2O, 8D2P, 8D2Q

  • PubMed Abstract: 

    Controlling the activity of the CRISPR-Cas9 system is essential to its safe adoption for clinical and research applications. Although the conformational dynamics of Cas9 are known to control its enzymatic activity, details of how Cas9 influences the catalytic processes at both nuclease domains remain elusive. Here we report five cryo-electron microscopy structures of the active Acidothermus cellulolyticus Cas9 complex along the reaction path at 2.2-2.9 Å resolution. We observed that a large movement in one nuclease domain, triggered by the cognate DNA, results in noticeable changes in the active site of the other domain that is required for metal coordination and catalysis. Furthermore, the conformations synchronize the reaction intermediates, enabling coupled cutting of the two DNA strands. Consistent with the roles of conformations in organizing the active sites, adjustments to the metal-coordination residues lead to altered metal specificity of A. cellulolyticus Cas9 and commonly used Streptococcus pyogenes Cas9 in cells.


  • Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease, Csn1 family1,138Acidothermus cellulolyticus 11BMutation(s): 0 
Gene Names: Acel_1951
UniProt
Find proteins for A0LWB3 (Acidothermus cellulolyticus (strain ATCC 43068 / DSM 8971 / 11B))
Explore A0LWB3 
Go to UniProtKB:  A0LWB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0LWB3
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
Single guide RNA (106-MER)106Acidothermus cellulolyticus 11B
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA target strand (5'-D(*AP*GP*CP*TP*TP*GP*GP*TP*GP*TP*AP*TP*A)-3')C [auth X]13synthetic construct
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA target strand (5'-D(P*CP*CP*AP*GP*GP*AP*TP*CP*TP*TP*GP*CP*CP*AP*TP*CP*CP*TP*AP*CP*CP*TP*CP*T)-3')D [auth T]24synthetic construct
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA non-target strand (5'-D(P*TP*AP*TP*AP*CP*AP*CP*CP*AP*AP*GP*CP*T)-3')E [auth D]13synthetic construct
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA non-target strand (5'-D(P*AP*GP*A)-3')F [auth Y]3synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM101343
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM099604

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references