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- EMDB-56124: Asp2Cas12l-sgRNA bound to target DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-56124
TitleAsp2Cas12l-sgRNA bound to target DNA
Map dataPhenix autosharpened local refinement map, covering complete structure.
Sample
  • Complex: Asp2Cas12l-crRNA bound to DNA
    • Protein or peptide: Asp2Cas12l
    • RNA: sgRNA (149-MER)
    • DNA: DNA (26-MER)
    • DNA: DNA (34-MER)
KeywordsCRISPR-Cas / Cas12 / HYDROLASE
Biological speciesArmatimonadota (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.51 Å
AuthorsSasnauskas G / Tamulaitiene G / Urbaitis T / Gasiunas G
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: CRISPR J / Year: 2026
Title: A Potent CRISPR-Cas12l Double-Strand Break Gene Editor.
Authors: Tomas Urbaitis / Laima Trinkuniene / Ieva Lenkaite / Monika Petrauskyte / Renatas Krasauskas / Migle Stitilyte / Modestas Sabaliauskas / Giedrius Sasnauskas / Giedre Tamulaitiene / Joshua K ...Authors: Tomas Urbaitis / Laima Trinkuniene / Ieva Lenkaite / Monika Petrauskyte / Renatas Krasauskas / Migle Stitilyte / Modestas Sabaliauskas / Giedrius Sasnauskas / Giedre Tamulaitiene / Joshua K Young / Virginijus Siksnys / Giedrius Gasiunas /
Abstract: Recently, a new family of CRISPR-Cas12 endonucleases from an unexplored phylum of bacteria, , was discovered. Named Cas12l, they are compact (800-900 aa), recognize a 5' C-rich protospacer adjacent ...Recently, a new family of CRISPR-Cas12 endonucleases from an unexplored phylum of bacteria, , was discovered. Named Cas12l, they are compact (800-900 aa), recognize a 5' C-rich protospacer adjacent motif, and present an N-terminal domain that stretches from the beginning to the end of the ribonucleoprotein-bound DNA target site, effectively locking it in place. Here, structure-guided rational design supplemented with AI-based large protein language model predictions was used to improve rates of DNA target cleavage of a family member, Asp2Cas12l. Compared to the wild-type, engineered variants exhibited an approximately 10-fold increase in double-strand break (DSB) editing efficiency in human cells with less target-to-target variation. Moreover, frequencies of editing were comparable to those of SpCas9 at overlapping target sites, and their DSBs efficiently corrected by homology-directed repair (39-56% of editing outcomes). Altogether, this study extends our understanding of CRISPR-Cas12 protein engineering and offers a potent new alternative for DSB-mediated genome editing in human cells.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Urbaitis T / Sasnauskas G / Tamulaitiene G / Gasiunas G
History
DepositionDec 19, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56124.png

Downloads & links

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Map

FileDownload / File: emd_56124.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhenix autosharpened local refinement map, covering complete structure.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å		1.1 Å/pix.
x 224 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.447
Minimum - Maximum-23.970303999999999 - 48.038876000000002
Average (Standard dev.)-0.000000000001957 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 246.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened local refinement map, covering complete structure.

Fileemd_56124_additional_1.map
AnnotationUnsharpened local refinement map, covering complete structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half A

Fileemd_56124_half_map_1.map
Annotationmap_half_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: map half B

Fileemd_56124_half_map_2.map
Annotationmap_half_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Asp2Cas12l-crRNA bound to DNA

EntireName: Asp2Cas12l-crRNA bound to DNA
Components
  • Complex: Asp2Cas12l-crRNA bound to DNA
    • Protein or peptide: Asp2Cas12l
    • RNA: sgRNA (149-MER)
    • DNA: DNA (26-MER)
    • DNA: DNA (34-MER)

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Supramolecule #1: Asp2Cas12l-crRNA bound to DNA

SupramoleculeName: Asp2Cas12l-crRNA bound to DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Armatimonadota (bacteria)

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Macromolecule #1: Asp2Cas12l

MacromoleculeName: Asp2Cas12l / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Armatimonadota (bacteria)
Molecular weightTheoretical: 99.348562 KDa
Recombinant expressionOrganism: Escherichia (bacteria)
SequenceString: MGKNRSSSSD LSPLERSLRK VGENRLERLR VREEKIRKHI EQHPRGKNDH QALHFLLHQI EVERNDLYRN LKDPEYVPKP AKQRRERRQ INVAKPPTRP KKEKGPQPES TKYVIRPPVP GKNLPAFASK YEARDTRDDS YQDGRSWTSA PYVEVELPIL G ADKVIQKL ...String:
MGKNRSSSSD LSPLERSLRK VGENRLERLR VREEKIRKHI EQHPRGKNDH QALHFLLHQI EVERNDLYRN LKDPEYVPKP AKQRRERRQ INVAKPPTRP KKEKGPQPES TKYVIRPPVP GKNLPAFASK YEARDTRDDS YQDGRSWTSA PYVEVELPIL G ADKVIQKL MKFVQKDERS IVRDWATKTY SSIEAAREAL LVGAQVSEDV SVWRGLLAET KNAQNFAALS DDQIEAAMSK EA KGADLRP RRAALLVAQR HWVDQTVKAI KESAPSGVDK DTLDRRLRAG LRGFHTAANS GKHTNPQFPY LTAEKPVVPM ESV VQSVLA FLDDPDDQRY TKDKEDDKKR HRVTVLQKEL GKARPRKRLE LQTPKWAGRP TVKGTISKRR DAALVWDTSK EANG LCLAL PIGGMPKIDV EQFIYQDGTS LLSDCQIASK TTKKGAACAV LPLKPKHDFL RWFTKHVENH NPDAPLERRC LHNTT QFVI VDPEGPRPRL FVRPVFKFYD PGKTVPNTHE TWKKPDCRYL VGIDRGINYV LRAVVVDTEE KKVIADIGLP GRKHEW RMI RDEIAYHQQM RDLARNTGKH ASVVAKHVRA LALARKKDRA LGKFATVEAV AELVKKCEQD YGSGNYCFVL EDLDMGA MN LKRNNRVKHM AVMEEALVNQ MRKQGYAYDG RRGRVDGVRH EGAWYTSQVS PFGWWAKRDE VEEAWKRDKT RPIGRKVG N WYEMPEPGQD GDRPDTYRKG YWSKPKNAEG KPYGRNRFSV EPGDEKPDAE RRFCWGSELF WDPNVKSFKG KEFPEGVVL DADFVGALNI ALRPLVNDGQ GKGFKAEDMA REHTILNPQF KIACQIPVYE FVEEDGDKWA ALRRIML

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Macromolecule #2: sgRNA (149-MER)

MacromoleculeName: sgRNA (149-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Armatimonadota (bacteria)
Molecular weightTheoretical: 52.888461 KDa
SequenceString:
UUAGGCGUUC CGUCUCGACU AUGCCGUACC ACUAGACCGA GCCUACACGG CACGCGGUCA UAGCGUUAAC CAAGGCGUGG UGACAAGCC UCUUUCAGGC GUCGGACACU UAAGAGCGUU GAAAAACGCU CUUAGGGAAU GAAAGGCCUU CAGAAGAGGG U GCAU

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Macromolecule #3: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.401233 KDa
SequenceString:
(DT)(DA)(DC)(DG)(DA)(DG)(DC)(DC)(DA)(DC) (DC)(DC)(DC)(DG)(DG)(DA)(DA)(DG)(DT)(DC) (DT)(DT)(DC)(DT)(DC)(DC)(DC)(DA)(DC) (DG)(DT)(DA)(DA)(DA)(DG)(DC)(DG)(DT)(DA) (DT) (DA)(DG)(DT)(DG)(DT)(DG)(DC)

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Macromolecule #4: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.481281 KDa
SequenceString:
(DG)(DC)(DA)(DC)(DA)(DC)(DT)(DA)(DT)(DA) (DC)(DG)(DG)(DA)(DA)(DA)(DT)(DG)(DC)(DA) (DC)(DC)(DC)(DT)(DC)(DT)(DT)(DC)(DT) (DG)(DA)(DA)(DG)(DG)(DC)(DG)(DG)(DG)(DT) (DG) (DG)(DC)(DT)(DC)(DG)(DT)(DA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 92000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.51 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 990101
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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