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- EMDB-60382: Cryo-EM structure of Cas12X2 with crRNA and Target DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-60382
TitleCryo-EM structure of Cas12X2 with crRNA and Target DNA
Map data
Sample
  • Complex: Ternary complex of Cas12X2 with crRNA and Target DNA
    • Protein or peptide: Cas12X2
    • RNA: CrRNA
    • DNA: TS
    • DNA: NTS
KeywordsCrispr-Cas12 / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesunclassified sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas12X2 with crRNA and Target DNA
Authors: Zhang X
History
DepositionJun 1, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60382.png

Downloads & links

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Map

FileDownload / File: emd_60382.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å		0.66 Å/pix.
x 384 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.085744746 - 0.22601454
Average (Standard dev.)0.00018226486 (±0.006626558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60382_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_60382_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 : Ternary complex of Cas12X2 with crRNA and Target DNA

EntireName: Ternary complex of Cas12X2 with crRNA and Target DNA
Components
  • Complex: Ternary complex of Cas12X2 with crRNA and Target DNA
    • Protein or peptide: Cas12X2
    • RNA: CrRNA
    • DNA: TS
    • DNA: NTS

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Supramolecule #1: Ternary complex of Cas12X2 with crRNA and Target DNA

SupramoleculeName: Ternary complex of Cas12X2 with crRNA and Target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unclassified sequences (unknown)

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Macromolecule #1: Cas12X2

MacromoleculeName: Cas12X2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 111.337992 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHMKKW LRSYDFSLEV SEEDTLHLLE CVKEYNELSK AYMDYMFKLK EDHKDDLDVC NLIERLQNGS GKELRALASC IFGGRKTSE DVFLRVKSYK KALVLIDSGE VKTYEDLSKS LGEKTGLRGT NSLFKEPKKE GKRKDRTGPL KEDQAKKINK M LAADLGIV ...String:
HHHHHHMKKW LRSYDFSLEV SEEDTLHLLE CVKEYNELSK AYMDYMFKLK EDHKDDLDVC NLIERLQNGS GKELRALASC IFGGRKTSE DVFLRVKSYK KALVLIDSGE VKTYEDLSKS LGEKTGLRGT NSLFKEPKKE GKRKDRTGPL KEDQAKKINK M LAADLGIV SALNLCQKGL LPIPEFAKNV EKLNKNVLYG IISQAGSRMK SFLKCDDLTQ QNHLNLKEIL KSYRLEYNLD EF QEQEASY QQWLSRMKSL NSFALTHRFL QGWAKRWRKQ FLAGKDPSWT LGEEATKICK EYQHLFVDND FIYLFGKEDL LKL KVEERK QNAQFTLPDV IKSPIYPQLG NNGQGFGIEQ VDNDIYLIIQ SCFIDRPNIR AKIVPHKKTS VWSLEQENTK QTKK KNAQI DKNKIPYKLF LRRAADRYEK QIEISECRLQ HRFCSGKANF HVVFSLKGEA NDTLTKASTL FLTATQKPVS EWSKD NLPK QMRVAFVDIG LNPPLSMSIY DYNQEDNSGE NLVYAGADQQ VPFGSANFVR EDQIGNVYNQ NLKRRIEELN DKIFYA SSC VSFYKNISSL EGATVELVGG RKVMCRQFDE EKVKDLYSVP VKALRELGLD HFFGLPEDLD QQNVEAATFY IENHIHH NK LTRKSFLSFR CKLWDYIHEK ILPEFSVIRN GRHFQFNKQF CSEAYSWMFL IHSMIRLKKS LSYSHSEPLK KGEPATFV F KNLQNYFNNF SKNVLKTVAA KLRDYCTTHN VSLCVVEDLE KFRTSSLNSK DKNRLLSIWS HRNVVQRFEE VLTEVGITI VSNDARHSSQ LDPVTMDWAY RDEQDKSKLW VKRDGEIFHI NADISSTQVQ AKRFFSRYAD IVYMKTLLKK DDNGSLRKLV VSDNSTRIQ SYLLRTINSK YAILEQDKLV PINQQEYNQI VGLKTSGVEE IYRHGESWVN LITHKTLQKE IGARTNVQ

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Macromolecule #2: CrRNA

MacromoleculeName: CrRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 17.95567 KDa
SequenceString:
GUGCUACAAG CGAAAAAGAU CGCUUGUGAU UUGCACUCCC CUACGUGCUG CUGAAG

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Macromolecule #3: TS

MacromoleculeName: TS / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 12.990339 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DA)(DA)(DA)(DG)(DT)(DC)(DA)(DG)(DC)(DA) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DG)(DG) (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DT)(DG)(DG) (DC) (DC)(DA)

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Macromolecule #4: NTS

MacromoleculeName: NTS / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 12.874235 KDa
SequenceString:
(DT)(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DC) (DT)(DC)(DC)(DC)(DC)(DT)(DA)(DC)(DG)(DT) (DG)(DC)(DT)(DG)(DC)(DT)(DG)(DA)(DC) (DT)(DT)(DT)(DG)(DC)(DA)(DA)(DG)(DG)(DG) (DC) (DA)(DG)

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81340
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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