8X5V | pdb_00008x5v

BlCas9-sgRNA-target DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.231 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8X5V

This is version 1.0 of the entry. See complete history

Literature

Structure and engineering of Brevibacillus laterosporus Cas9.

Nakane, T.Nakagawa, R.Ishiguro, S.Okazaki, S.Mori, H.Shuto, Y.Yamashita, K.Yachie, N.Nishimasu, H.Nureki, O.

(2024) Commun Biol 7: 803-803

  • DOI: https://doi.org/10.1038/s42003-024-06422-z
  • Primary Citation Related Structures: 
    8X5V

  • PubMed Abstract: 

    The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets complementary to an RNA guide, and is widely used as a powerful genome-editing tool. Here, we report the crystal structure of Brevibacillus laterosporus Cas9 (BlCas9, also known as BlatCas9), in complex with a guide RNA and its target DNA at 2.4-Å resolution. The structure reveals that the BlCas9 guide RNA adopts an unexpected architecture containing a triple-helix, which is specifically recognized by BlCas9, and that BlCas9 recognizes a unique N 4 CNDN protospacer adjacent motif through base-specific interactions on both the target and non-target DNA strands. Based on the structure, we rationally engineered a BlCas9 variant that exhibits enhanced genome- and base-editing activities with an expanded target scope in human cells. This approach may further improve the performance of the enhanced BlCas9 variant to generate useful genome-editing tools that require only a single C PAM nucleotide and can be packaged into a single AAV vector for in vivo gene therapy.


  • Organizational Affiliation
    • Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 156.46 kDa 
  • Atom Count: 10,610 
  • Modeled Residue Count: 1,034 
  • Deposited Residue Count: 1,079 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BlCas9933Brevibacillus laterosporusMutation(s): 0 
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (110-mer)110Brevibacillus laterosporus
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (28-mer)28synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (8-mer)8synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
V [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
FA [auth B]
G [auth A]
GA [auth B]
E [auth A],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth C],
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]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
EA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.231 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.204 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.75α = 90
b = 99.21β = 97.087
c = 119.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)Japan23ama121012

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release