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- EMDB-62606: Cas12a-PCPS-dark -

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Basic information

Entry
Database: EMDB / ID: EMD-62606
TitleCas12a-PCPS-dark
Map data
Sample
  • Complex: Cas12a-PCPS-dark
    • Protein or peptide: LbCas12a
    • RNA: RNA (27-MER)
    • RNA: RNA (5'-R(P*AP*AP*AP*CP*CP*CP*C)-3')
KeywordsCas12a-PCPS-dark / DNA BINDING PROTEIN/RNA / DNA BINDING PROTEIN-RNA complex
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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZhang MF
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Commun / Year: 2025
Title: Scalable modulation of CRISPR‒Cas enzyme activity using photocleavable phosphorothioate DNA.
Authors: Menglu Hu / Bingni Zhang / Yuanyue Shan / Feng Cao / Yihui Wang / Weiwei Qi / Xue Wang / Yuting Shen / Xinyi Guo / Mengmeng Zhang / Tian Tian / Wei Xie / Mingfeng Zhang / Fang Liang / ...Authors: Menglu Hu / Bingni Zhang / Yuanyue Shan / Feng Cao / Yihui Wang / Weiwei Qi / Xue Wang / Yuting Shen / Xinyi Guo / Mengmeng Zhang / Tian Tian / Wei Xie / Mingfeng Zhang / Fang Liang / Duanqing Pei / Xiaoming Zhou /
Abstract: The regulation of CRISPR‒Cas activity is critical for developing advanced biotechnologies. Optical control of CRISPR‒Cas system activity can be achieved by modulation of Cas proteins or guide RNA ...The regulation of CRISPR‒Cas activity is critical for developing advanced biotechnologies. Optical control of CRISPR‒Cas system activity can be achieved by modulation of Cas proteins or guide RNA (gRNA), but these approaches either require complex protein engineering modifications or customization of the optically modulated gRNAs according to the target. Here, we present a method, termed photocleavable phosphorothioate DNA (PC&PS DNA)-mediated regulation of CRISPR‒Cas activity (DNACas), that is versatile and overcomes the limitations of conventional methods. In DNACas, CRISPR‒Cas activity is silenced by the affinity binding of PC&PS DNA and restored through light-triggered chemical bond breakage of PC&PS DNA. The universality of DNACas is demonstrated by adopting the PC&PS DNA to regulate various CRISPR‒Cas enzymes, achieving robust light-switching performance. DNACas is further adopted to develop a light-controlled one-pot LAMP-BrCas12b detection method and a spatiotemporal gene editing strategy. We anticipate that DNACas could be employed to drive various biotechnological advances.
History
DepositionDec 5, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62606.png

Downloads & links

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Map

FileDownload / File: emd_62606.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 512 pix.
= 291.84 Å		0.57 Å/pix.
x 512 pix.
= 291.84 Å		0.57 Å/pix.
x 512 pix.
= 291.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.57 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.6024731 - 0.88625187
Average (Standard dev.)-0.00006291332 (±0.015934259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 291.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62606_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_62606_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 : Cas12a-PCPS-dark

EntireName: Cas12a-PCPS-dark
Components
  • Complex: Cas12a-PCPS-dark
    • Protein or peptide: LbCas12a
    • RNA: RNA (27-MER)
    • RNA: RNA (5'-R(P*AP*AP*AP*CP*CP*CP*C)-3')

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Supramolecule #1: Cas12a-PCPS-dark

SupramoleculeName: Cas12a-PCPS-dark / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)

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Macromolecule #1: LbCas12a

MacromoleculeName: LbCas12a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lachnospiraceae bacterium ND2006 (bacteria)
Molecular weightTheoretical: 143.489859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKLEKFTNCY SLSKTLRFKA IPVGKTQENI DNKRLLVEDE KRAEDYKGVK KLLDRYYLSF INDVLHSIKL KNLNNYISLF RKKTRTEKE NKELENLEIN LRKEIAKAFK GNEGYKSLFK KDIIETILPE FLDDKDEIAL VNSFNGFTTA FTGFFDNREN M FSEEAKST ...String:
SKLEKFTNCY SLSKTLRFKA IPVGKTQENI DNKRLLVEDE KRAEDYKGVK KLLDRYYLSF INDVLHSIKL KNLNNYISLF RKKTRTEKE NKELENLEIN LRKEIAKAFK GNEGYKSLFK KDIIETILPE FLDDKDEIAL VNSFNGFTTA FTGFFDNREN M FSEEAKST SIAFRCINEN LTRYISNMDI FEKVDAIFDK HEVQEIKEKI LNSDYDVEDF FEGEFFNFVL TQEGIDVYNA II GGFVTES GEKIKGLNEY INLYNQKTKQ KLPKFKPLYK QVLSDRESLS FYGEGYTSDE EVLEVFRNTL NKNSEIFSSI KKL EKLFKN FDEYSSAGIF VKNGPAISTI SKDIFGEWNV IRDKWNAEYD DIHLKKKAVV TEKYEDDRRK SFKKIGSFSL EQLQ EYADA DLSVVEKLKE IIIQKVDEIY KVYGSSEKLF DADFVLEKSL KKNDAVVAIM KDLLDSVKSF ENYIKAFFGE GKETN RDES FYGDFVLAYD ILLKVDHIYD AIRNYVTQKP YSKDKFKLYF QNPQFMGGWD KDKETDYRAT ILRYGSKYYL AIMDKK YAK CLQKIDKDDV NGNYEKINYK LLPGPNKMLP KVFFSKKWMA YYNPSEDIQK IYKNGTFKKG DMFNLNDCHK LIDFFKD SI SRYPKWSNAY DFNFSETEKY KDIAGFYREV EEQGYKVSFE SASKKEVDKL VEEGKLYMFQ IYNKDFSDKS HGTPNLHT M YFKLLFDENN HGQIRLSGGA ELFMRRASLK KEELVVHPAN SPIANKNPDN PKKTTTLSYD VYKDKRFSED QYELHIPIA INKCPKNIFK INTEVRVLLK HDDNPYVIGI DRGERNLLYI VVVDGKGNIV EQYSLNEIIN NFNGIRIKTD YHSLLDKKEK ERFEARQNW TSIENIKELK AGYISQVVHK ICELVEKYDA VIALEDLNSG FKNSRVKVEK QVYQKFEKML IDKLNYMVDK K SNPCATGG ALKGYQITNK FESFKSMSTQ NGFIFYIPAW LTSKIDPSTG FVNLLKTKYT SIADSKKFIS SFDRIMYVPE ED LFEFALD YKNFSRTDAD YIKKWKLYSY GNRIRIFRNP KKNNVFDWEE VCLTSAYKEL FNKYGINYQQ GDIRALLCEQ SDK AFYSSF MALMSLMLQM RNSITGRTDV DFLISPVKNS DGIFYDSRNY EAQENAILPK NADANGAYNI ARKVLWAIGQ FKKA EDEKL DKVKIAISNK EWLEYAQTSV

UniProtKB: LbCas12a

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Macromolecule #2: RNA (27-MER)

MacromoleculeName: RNA (27-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.654111 KDa
SequenceString:
AAUUUCUACU AAGUGUAGAU GGGGUUU

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Macromolecule #3: RNA (5'-R(P*AP*AP*AP*CP*CP*CP*C)-3')

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*CP*CP*CP*C)-3') / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.163387 KDa
SequenceString:
AAACCCC

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI MORGAGNI
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 160000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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