6NBT

CRISPR Complex Subunit Csm3 from Staphylococcus epidermidis RP62a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM.

Dorsey, B.W.Huang, L.Mondragon, A.

(2019) Nucleic Acids Res. 47: 3765-3783

  • DOI: 10.1093/nar/gkz079
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas systems are classified into different classes and ty ...

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas systems are classified into different classes and types. Class 1 CRISPR-Cas systems form multi-protein effector complexes that includes a guide RNA (crRNA) used to identify the target for destruction. Here we present crystal structures of Staphylococcus epidermidis Type III-A CRISPR subunits Csm2 and Csm3 and a 5.2 Å resolution single-particle cryo-electron microscopy (cryo-EM) reconstruction of an in vivo assembled effector subcomplex including the crRNA. The structures help to clarify the quaternary architecture of Type III-A effector complexes, and provide details on crRNA binding, target RNA binding and cleavage, and intermolecular interactions essential for effector complex assembly. The structures allow a better understanding of the organization of Type III-A CRISPR effector complexes as well as highlighting the overall similarities and differences with other Class 1 effector complexes.


    Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CRISPR-associated protein
A, B
238Staphylococcus epidermidis (strain ATCC 35984 / RP62A)Mutation(s): 0 
Find proteins for Q5HK91 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Go to UniProtKB:  Q5HK91
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SM
Query on SM

Download SDF File 
Download CCD File 
A, B
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.612α = 90.00
b = 50.979β = 97.05
c = 83.018γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
CRANK2phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM118108

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-02-27
    Type: Data collection, Database references
  • Version 1.2: 2019-05-01
    Type: Data collection, Database references