6JDJ

Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9

• PDB DOI:  https://doi.org/10.2210/pdb6JDJ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Neisseria meningitidis 8013
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-01 Released: 2019-05-15 
• Deposition Author(s): Cheng, Z., Huang, X., Sun, W., Wang, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.227 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2.

Thavalingam, A., Cheng, Z., Garcia, B., Huang, X., Shah, M., Sun, W., Wang, M., Harrington, L., Hwang, S., Hidalgo-Reyes, Y., Sontheimer, E.J., Doudna, J., Davidson, A.R., Moraes, T.F., Wang, Y., Maxwell, K.L.

(2019) Nat Commun 10: 2806-2806

• PubMed: 31243272 
• DOI: https://doi.org/10.1038/s41467-019-10577-3
• Primary Citation of Related Structures:  
  6JD7, 6JDJ, 6JDX, 6N05


• PubMed Abstract: 
  

CRISPR-Cas adaptive immune systems function to protect bacteria from invasion by foreign genetic elements. The CRISPR-Cas9 system has been widely adopted as a powerful genome-editing tool, and phage-encoded inhibitors, known as anti-CRISPRs, offer a means of regulating its activity. Here, we report the crystal structures of anti-CRISPR protein AcrIIC2 _Nme alone and in complex with Nme1Cas9. We demonstrate that AcrIIC2 _Nme inhibits Cas9 through interactions with the positively charged bridge helix, thereby preventing sgRNA loading. In vivo phage plaque assays and in vitro DNA cleavage assays show that AcrIIC2 _Nme mediates its activity through a large electronegative surface. This work shows that anti-CRISPR activity can be mediated through the inhibition of Cas9 complex assembly.

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Organizational Affiliation: 

Department of Biochemistry, University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON, M5G 1M1, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.18 kDa 
• Atom Count: 2,337 
• Modelled Residue Count: 289 
• Deposited Residue Count: 326 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AcrIIC2	A, B	124	Neisseria meningitidis 8013	Mutation(s): 0  Gene Names: CIJ84_02100

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	C	78	Neisseria meningitidis 8013	Mutation(s): 0  Gene Names: cas9, NMV_1993 EC: 3.1
UniProt
Find proteins for C9X1G5 (Neisseria meningitidis serogroup C (strain 8013)) Explore C9X1G5  Go to UniProtKB:  C9X1G5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.227 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.439	α = 90
b = 77.347	β = 90
c = 106.885	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Cheng, Z., Huang, X., Sun, W., Wang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31725008

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-07-31
  Changes: Data collection, Database references