9MK3 | pdb_00009mk3

Engineered AsCas12a (M537R, F870L)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.198 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanistic basis for improved activity of Engineered AsCas12a.

Jansson-Fritzberg, L.Chica, B.Latrick, C.Olland, A.Dementiev, A.White, A.Kutter, S.Lemercier, J.N.Wolk, S.

(2026) Commun Biol 

  • DOI: https://doi.org/10.1038/s42003-026-09799-1
  • Primary Citation Related Structures: 
    9MK3

  • PubMed Abstract: 

    CRISPR-associated proteins (Cas) are central to gene editing, forming nuclease complexes with guide RNA to enable precise genome modification. Among numerous Cas variants, Cas9 and Cas12a are the most extensively studied. While much is known about the genomic substrates for these enzymes, less is known about the determinants of the DNA cleavage activity. Wild-type Cas12a exhibits higher intrinsic specificity than Cas9, minimizing off-target activity, but lower overall potency. Recent protein engineering has sought to improve both parameters. Here, we shed light on the structural and mechanistic basis by which an engineered AsCas12a variant achieves high potency while retaining its hallmark specificity. We show that reduced protein-DNA interactions facilitate more rapid R-loop formation, thereby enhancing cleavage activity. These results provide mechanistic insight into Cas12a function and highlight strategies for designing genome-editing nucleases with optimal balance between efficiency and specificity.


  • Organizational Affiliation
    • Editas Medicine, Inc, Cambridge, MA, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated endonuclease Cas12a
A, E
1,307AcidaminococcusMutation(s): 2 
Gene Names: cas12acpf1HMPREF1246_0236
EC: 3.1.21.1 (PDB Primary Data), 4.6.1.22 (PDB Primary Data)
UniProt
Find proteins for U2UMQ6 (Acidaminococcus sp. (strain BV3L6))
Explore U2UMQ6 
Go to UniProtKB:  U2UMQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU2UMQ6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
gRNA (41-MER)
B, F
44Acidaminococcus
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
TS DNA (31-MER)
C, G
34Acidaminococcus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
NTS DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*T)-3')
D, H
10Acidaminococcus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
T [auth E],
U [auth E],
V [auth E],
W [auth G]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth A],
S [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
R [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.240 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.198 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.916α = 90
b = 198.585β = 95.272
c = 140.363γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-03-25
    Changes: Database references