6KC8

Crystal structure of WT Nme1Cas9 in complex with sgRNA and target DNA (ATATGATT PAM) in post-cleavage state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States.

Sun, W.Yang, J.Cheng, Z.Amrani, N.Liu, C.Wang, K.Ibraheim, R.Edraki, A.Huang, X.Wang, M.Wang, J.Liu, L.Sheng, G.Yang, Y.Lou, J.Sontheimer, E.J.Wang, Y.

(2019) Mol.Cell --: --

  • DOI: 10.1016/j.molcel.2019.09.025
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of menin ...

    High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China. Electronic address: ylwang@ibp.ac.cn.,RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.,RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address: erik.sontheimer@umassmed.edu.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated endonuclease Cas9
A
1083Neisseria meningitidis serogroup C (strain 8013)Mutation(s): 0 
Gene Names: cas9
EC: 3.1.-.-
Find proteins for C9X1G5 (Neisseria meningitidis serogroup C (strain 8013))
Go to UniProtKB:  C9X1G5
Entity ID: 2
MoleculeChainsLengthOrganism
sgRNAB135synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*AP*GP*TP*TP*AP*AP*AP*TP*AP*GP*CP*AP*GP*AP*GP*TP*GP*AP*CP*C)-3')C21synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*AP*TP*GP*AP*TP*TP*TP*TP*A)-3')D11synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*AP*AP*AP*TP*CP*AP*TP*AP*TP*GP*TP*A)-3')P14synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 131.604α = 90.00
b = 159.517β = 90.00
c = 117.963γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31725008

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Data collection, Database references