5W1H | pdb_00005w1h

Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (24-nt spacer)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.216 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5W1H

This is version 1.4 of the entry. See complete history

Literature

Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.

Knott, G.J.East-Seletsky, A.Cofsky, J.C.Holton, J.M.Charles, E.O'Connell, M.R.Doudna, J.A.

(2017) Nat Struct Mol Biol 24: 825-833

  • DOI: https://doi.org/10.1038/nsmb.3466
  • Primary Citation Related Structures: 
    5W1H, 5W1I, 5WLH

  • PubMed Abstract: 

    CRISPR adaptive immune systems protect bacteria from infections by deploying CRISPR RNA (crRNA)-guided enzymes to recognize and cut foreign nucleic acids. Type VI-A CRISPR-Cas systems include the Cas13a enzyme, an RNA-activated RNase capable of crRNA processing and single-stranded RNA degradation upon target-transcript binding. Here we present the 2.0-Å resolution crystal structure of a crRNA-bound Lachnospiraceae bacterium Cas13a (LbaCas13a), representing a recently discovered Cas13a enzyme subtype. This structure and accompanying biochemical experiments define the Cas13a catalytic residues that are directly responsible for crRNA maturation. In addition, the orientation of the foreign-derived target-RNA-specifying sequence in the protein interior explains the conformational gating of Cas13a nuclease activation. These results describe how Cas13a enzymes generate functional crRNAs and how catalytic activity is blocked before target-RNA recognition, with implications for both bacterial immunity and diagnostic applications.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.

Macromolecule Content 

  • Total Structure Weight: 189.28 kDa 
  • Atom Count: 12,499 
  • Modeled Residue Count: 1,343 
  • Deposited Residue Count: 1,492 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LbaCas13a (C2c2)1,440Lachnospiraceae bacteriumMutation(s): 0 
Gene Names: NK4A179
UniProt
Find proteins for A0A2D0TCG9 (Lachnospiraceae bacterium)
Explore A0A2D0TCG9 
Go to UniProtKB:  A0A2D0TCG9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TCG9
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
mature crRNA52Lachnospiraceae bacterium
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
AA [auth A],
BA [auth A],
Z [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.216 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.842α = 90
b = 92.213β = 92.42
c = 115.858γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
SHELXCDphasing
SHELXDEphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Database references
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references