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- EMDB-60385: Cryo-EM structure of Cas12X with crRNA and Target DNA, Conformation 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-60385
TitleCryo-EM structure of Cas12X with crRNA and Target DNA, Conformation 3
Map data
Sample
  • Complex: Ternary complex of Cas12X with crRNA and Target DNA
    • RNA: RNA (60-MER)
    • DNA: DNA (44-MER)
    • Protein or peptide: Cas12X
    • DNA: DNA (44-MER)
KeywordsCrispr-Cas12 / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesunclassified sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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 Cas12X with crRNA and Target DNA, Conformation 3
Authors: Zhang X
History
DepositionJun 3, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60385.png

Downloads & links

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Map

FileDownload / File: emd_60385.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: 0.05
Minimum - Maximum-0.12739536 - 0.29936555
Average (Standard dev.)0.00009441232 (±0.007541206)
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: #1

Fileemd_60385_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60385_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 Cas12X with crRNA and Target DNA

EntireName: Ternary complex of Cas12X with crRNA and Target DNA
Components
  • Complex: Ternary complex of Cas12X with crRNA and Target DNA
    • RNA: RNA (60-MER)
    • DNA: DNA (44-MER)
    • Protein or peptide: Cas12X
    • DNA: DNA (44-MER)

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Supramolecule #1: Ternary complex of Cas12X with crRNA and Target DNA

SupramoleculeName: Ternary complex of Cas12X with crRNA and Target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: unclassified sequences (unknown)

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Macromolecule #1: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 19.229471 KDa
SequenceString:
GUGCUGCUGU CUCCCAGACG GGAGGCAGAA CUGCACCUUC CAUCAGAGAA CCUCACUGCG

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Macromolecule #2: DNA (44-MER)

MacromoleculeName: DNA (44-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 13.644746 KDa
SequenceString:
(DC)(DA)(DA)(DG)(DC)(DC)(DG)(DT)(DC)(DT) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DA)(DG)(DG) (DT)(DT)(DC)(DT)(DC)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DA)(DG)(DC)(DA)(DT)(DA)(DT) (DC) (DG)(DT)(DA)(DG)

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Macromolecule #4: DNA (44-MER)

MacromoleculeName: DNA (44-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 13.453643 KDa
SequenceString:
(DC)(DT)(DA)(DC)(DG)(DA)(DT)(DA)(DT)(DG) (DC)(DT)(DT)(DC)(DC)(DA)(DT)(DC)(DA)(DG) (DA)(DG)(DA)(DA)(DC)(DC)(DT)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DA)(DG)(DA)(DC)(DG) (DG) (DC)(DT)(DT)(DG)

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Macromolecule #3: Cas12X

MacromoleculeName: Cas12X / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 106.402023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: HHHHHHMPSY KSSRVLVRDV PEELVDHYER SHRVAAFFMR LLLAMRREPY SLRMRDGTER EVDLDETDDF LRSAGCEEPD AVSDDLRSF ALAVLHQDNP KKRAFLESEN CVSILCLEKS ASGTRYYKRP GYQLLKKAIE EEWGWDKFEA SLLDERTGEV A EKFAALSM ...String:
HHHHHHMPSY KSSRVLVRDV PEELVDHYER SHRVAAFFMR LLLAMRREPY SLRMRDGTER EVDLDETDDF LRSAGCEEPD AVSDDLRSF ALAVLHQDNP KKRAFLESEN CVSILCLEKS ASGTRYYKRP GYQLLKKAIE EEWGWDKFEA SLLDERTGEV A EKFAALSM EDWRRFFAAR DPDDLGRELL KTDTREGMAA ALRLRERGVF PVSVPEHLDL DSLKAAMASA AERLKSWLAC NQ RAVDEKS ELRKRFEEAL DGVDPEKYAL FEKFAAELQQ ADYNVTKKLV LAVSAKFPAT EPSEFKRGVE ILKEDGYKPL WED FRELGF VYLAERKWER RRGGAAVTLC DADDSPIKVR FGLTGRGRKF VLSAAGSRFL ITVKLPCGDV GLTAVPSRYF WNPS VGRTT SNSFRIEFTK RTTENRRYVG EVKEIGLVRQ RGRYYFFIDY NFDPEEVSDE TKVGRAFFRA PLNESRPKPK DKLTV MGID LGINPAFAFA VCTLGECQDG IRSPVAKMED VSFDSTGLRG GIGSQKLHRE MHNLSDRCFY GARYIRLSKK LRDRGA LND IEARLLEEKY IPGFRIVHIE DADERRRTVG RTVKEIKQEY KRIRHQFYLR YHTSKRDRTE LISAEYFRML FLVKNLR NL LKSWNRYHWT TGDRERRGGN PDELKSYVRY YNNLRMDTLK KLTCAIVRTA KEHGATLVAM ENIQRVDRDD EVKRRKEN S LLSLWAPGMV LERVEQELKN EGILAWEVDP RHTSQTSCIT DEFGYRSLVA KDTFYFEQDR KIHRIDADVN AAINIARRF LTRYRSLTQL WASLLDDGRY LVNVTRQHER AYLELQTGAP AATLNPTAEA SYELVGLSPE EEELAQTRIK RKKREPFYRH EGVWLTREK HREQVHELRN QVLALGNAKI PEIRT

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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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88876
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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