5ZYF

Crystal structure of Streptococcus pyogenes type II-A Cas2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2

Ka, D.Jang, D.M.Han, B.W.Bae, E.

(2018) Nucleic Acids Res 46: 9805-9815

  • DOI: https://doi.org/10.1093/nar/gky702
  • Primary Citation of Related Structures:  
    5ZYF

  • PubMed Abstract: 

    Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR-Cas systems, the Cas1-Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.


  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endoribonuclease Cas2
A, B, C, D, E
A, B, C, D, E, F
92Streptococcus pyogenes serotype M1Mutation(s): 0 
Gene Names: cas2SPy_1048
EC: 3.1
UniProt
Find proteins for Q99ZW0 (Streptococcus pyogenes serotype M1)
Explore Q99ZW0 
Go to UniProtKB:  Q99ZW0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99ZW0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
M [auth B]
P [auth C]
Q [auth C]
R [auth C]
G [auth A],
M [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
T [auth E],
U [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.771α = 90
b = 75.292β = 90
c = 145.702γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
PHENIXmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2018-08-15 
  • Deposition Author(s): Ka, D., Bae, E.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1D1A1A09916821
Rural Development AdministrationKorea, Republic OfPJ013181

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references