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- EMDB-66115: Cryo-EM structure of the LbCas12a-Lid2-crRNA-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-66115
TitleCryo-EM structure of the LbCas12a-Lid2-crRNA-DNA complex
Map data
Sample
  • Complex: LbCas12a-Lid2.3-crRNA-target DNA
    • Complex: crRNA-target DNA
      • RNA: crRNA
      • DNA: DNA (39-MER)
      • DNA: DNA (39-MER)
    • Complex: LbCas12a-Lid2.3
      • Protein or peptide: Cpf1
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsCRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN
Function / homology
Function and homology information


: / CRISPR-associated endonuclease Cpf1 PI domain / : / CRISPR-associated endonuclease Cpf1 REC2 domain / CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsOmura SN / Warren Villegas R / Van der Oost J / Nureki O / Warren VR / Hirano H / Kusakizako T / Kise Y / Lebbink HGJ / Itoh Y
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Engineering and characterization of a novel Cas12a nickase
Authors: Warren Villegas R / Omura SN / Castro DR / Sudfeld C / Luteijn M / Morinaga H / Inoue WJ / Shuto Y / Vleesschauwer DD / Staals RHJ / Nureki O / Wu WY / Van der Oost J
History
DepositionSep 4, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66115.png

Downloads & links

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Map

FileDownload / File: emd_66115.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 162 pix.
= 161.352 Å		1 Å/pix.
x 162 pix.
= 161.352 Å		1 Å/pix.
x 162 pix.
= 161.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.5017494 - 0.84955704
Average (Standard dev.)0.001795182 (±0.026070332)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin696969
Dimensions162162162
Spacing162162162
CellA=B=C: 161.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66115_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66115_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66115_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LbCas12a-Lid2.3-crRNA-target DNA

EntireName: LbCas12a-Lid2.3-crRNA-target DNA
Components
  • Complex: LbCas12a-Lid2.3-crRNA-target DNA
    • Complex: crRNA-target DNA
      • RNA: crRNA
      • DNA: DNA (39-MER)
      • DNA: DNA (39-MER)
    • Complex: LbCas12a-Lid2.3
      • Protein or peptide: Cpf1
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: LbCas12a-Lid2.3-crRNA-target DNA

SupramoleculeName: LbCas12a-Lid2.3-crRNA-target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)

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Supramolecule #2: crRNA-target DNA

SupramoleculeName: crRNA-target DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#4

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Supramolecule #3: LbCas12a-Lid2.3

SupramoleculeName: LbCas12a-Lid2.3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1

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Macromolecule #1: Cpf1

MacromoleculeName: Cpf1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Molecular weightTheoretical: 144.912234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH ENLYFQSNAS KLEKFTNCYS LSKTLRFKAI PVGKTQENID NKRLLVEDEK RAEDYKGVKK LLDRYYLSFI NDVLHSIKL KNLNNYISLF RKKTRTEKEN KELENLEINL RKEIAKAFKG NEGYKSLFKK DIIETILPEF LDDKDEIALV N SFNGFTTA ...String:
MGSSHHHHHH ENLYFQSNAS KLEKFTNCYS LSKTLRFKAI PVGKTQENID NKRLLVEDEK RAEDYKGVKK LLDRYYLSFI NDVLHSIKL KNLNNYISLF RKKTRTEKEN KELENLEINL RKEIAKAFKG NEGYKSLFKK DIIETILPEF LDDKDEIALV N SFNGFTTA FTGFFDNREN MFSEEAKSTS IAFRCINENL TRYISNMDIF EKVDAIFDKH EVQEIKEKIL NSDYDVEDFF EG EFFNFVL TQEGIDVYNA IIGGFVTESG EKIKGLNEYI NLYNQKTKQK LPKFKPLYKQ VLSDRESLSF YGEGYTSDEE VLE VFRNTL NKNSEIFSSI KKLEKLFKNF DEYSSAGIFV KNGPAISTIS KDIFGEWNVI RDKWNAEYDD IHLKKKAVVT EKYE DDRRK SFKKIGSFSL EQLQEYADAD LSVVEKLKEI IIQKVDEIYK VYGSSEKLFD ADFVLEKSLK KNDAVVAIMK DLLDS VKSF ENYIKAFFGE GKETNRDESF YGDFVLAYDI LLKVDHIYDA IRNYVTQKPY SKDKFKLYFQ NPQFMGGWDK DKETDY RAT ILRYGSKYYL AIMDKKYAKC LQKIDKDDVN GNYEKINYKL LPGPNKMLPK VFFSKKWMAY YNPSEDIQKI YKNGTFK KG DMFNLNDCHK LIDFFKDSIS RYPKWSNAYD FNFSETEKYK DIAGFYREVE EQGYKVSFES ASKKEVDKLV EEGKLYMF Q IYNKDFSDKS HGTPNLHTMY FKLLFDENNH GQIRLSGGAE LFMRRASLKK EELVVHPANS PIANKNPDNP KKTTTLSYD VYKDKRFSED QYELHIPIAI NKCPKNIFKI NTEVRVLLKH DDNPYVIGID RGERNLLYIV VVDGKGNIVE QYSLNEIINN FNGIRIKTD YHSLLDKKEK ERFEARQNWT SIENIKELKA GYISQVVHKI CELVEKYDAV IALEDLNSYC SSVYQKFEKM L IDKLNYMV DKKSNPCATG GALKGYQITN KFESFKSMST QNGFIFYIPA WLTSKIDPST GFVNLLKTKY TSIADSKKFI SS FDRIMYV PEEDLFEFAL DYKNFSRTDA DYIKKWKLYS YGNRIRIFRN PKKNNVFDWE EVCLTSAYKE LFNKYGINYQ QGD IRALLC EQSDKAFYSS FMALMSLMLQ MRNSITGRTD VDFLISPVKN SDGIFYDSRN YEAQENAILP KNADANGAYN IARK VLWAI GQFKKAEDEK LDKVKIAISN KEWLEYAQTS VK

UniProtKB: Cpf1

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Macromolecule #2: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Molecular weightTheoretical: 13.433973 KDa
SequenceString:
GGAAUUUCUA CUAAGUGUAG AUCUACAUGC UACAGUGCUA GC

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Macromolecule #3: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Molecular weightTheoretical: 12.137806 KDa
SequenceString:
(DG)(DG)(DT)(DG)(DA)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DT)(DG) (DT)(DA)(DG)(DC)(DA)(DT)(DG)(DT)(DA) (DG)(DT)(DA)(DA)(DA)(DG)(DG)(DA)(DC)(DG)

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Macromolecule #4: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Molecular weightTheoretical: 11.870622 KDa
SequenceString:
(DC)(DG)(DT)(DC)(DC)(DT)(DT)(DT)(DA)(DC) (DT)(DA)(DC)(DA)(DT)(DG)(DC)(DT)(DA)(DC) (DA)(DG)(DT)(DG)(DC)(DT)(DA)(DG)(DC) (DC)(DG)(DT)(DA)(DG)(DT)(DC)(DA)(DC)(DC)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 19 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5xuu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 100683
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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