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- EMDB-37788: Cryo-EM structure of Cas12-1 with 5 nt complementary heteroduplex -

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Basic information

Entry
Database: EMDB / ID: EMD-37788
TitleCryo-EM structure of Cas12-1 with 5 nt complementary heteroduplex
Map data
Sample
  • Complex: The ternary complex of Cas12-1 with 5 nt complementary heteroduplex
    • Protein or peptide: Cas12-1
    • RNA: RNA
    • DNA: TS
    • DNA: NTS
KeywordsCirspr-Cas12 family / RNA BINDING PROTEIN-RNA-DNA COMPLEX
Biological speciesunclassified sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsKuo Z / Xi Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32188102 to J.-K.Z. China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas12-1 with 5 nt complementary heteroduplex
Authors: Kuo Z / Xi Z
History
DepositionOct 16, 2023-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37788.png

Downloads & links

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Map

FileDownload / File: emd_37788.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: 0.02
Minimum - Maximum-0.0539813 - 2.3186076
Average (Standard dev.)0.0006604144 (±0.01660675)
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_37788_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_37788_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 : The ternary complex of Cas12-1 with 5 nt complementary heteroduplex

EntireName: The ternary complex of Cas12-1 with 5 nt complementary heteroduplex
Components
  • Complex: The ternary complex of Cas12-1 with 5 nt complementary heteroduplex
    • Protein or peptide: Cas12-1
    • RNA: RNA
    • DNA: TS
    • DNA: NTS

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Supramolecule #1: The ternary complex of Cas12-1 with 5 nt complementary heteroduplex

SupramoleculeName: The ternary complex of Cas12-1 with 5 nt complementary heteroduplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unclassified sequences (unknown)

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Macromolecule #1: Cas12-1

MacromoleculeName: Cas12-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 83.449094 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTPKTETPVG ALIKKFFPGK RFQKNYLKDA GKKLKREGEA AAVEYLSGKQ EDHPANFCPP AKVNILAQSR PLSEWPINLV SKGVQEYVY GLTAAEREAN GDFGTSRKSL DRWFARTGVP THGYTTVQGL NLILRHTFNR YDGVIKKVET RNEKRRSKAT R INVSREAD ...String:
MTPKTETPVG ALIKKFFPGK RFQKNYLKDA GKKLKREGEA AAVEYLSGKQ EDHPANFCPP AKVNILAQSR PLSEWPINLV SKGVQEYVY GLTAAEREAN GDFGTSRKSL DRWFARTGVP THGYTTVQGL NLILRHTFNR YDGVIKKVET RNEKRRSKAT R INVSREAD GLPPIEAEPE ETAFGPDGKL KERPGINPSI YCYQQVSPVP YNPAKHPALP FSGVDPGAPL PLGTPNRLSI PK GQPGYVP EWQRPHLSTK NKRIRKWYAR ANWRRKPGRK SVLDEAKLKE AALKEAIPII VTIGKDWIVM DARGLLRAVY WRG IAKPGL SLKELLGFFS GDPVLDPKRG IATFTFKLGA VAVHSRKPTR GKKSKELLLS MTAEKPHVGL VAIDLGQTNP VAAE FSRVK REGETLQAEP LGQIVLPDDL VKDLTRYRRA WDATEEQIKA EAIVQLPEEC RAEVVKVNQM SAEETKHLIL DRGVS GDLP WEKMTSNTTF ISDHLLAKGV TDQVFFEKKS KGKKKGTETV KRKDYGWVKL LRPRLSQETR KAVNDKTWEL KRASTE YVR LSRRKTELAR RCVNYIVRET KRWTQCEDIA IVIEDLNVRF FHGSGERPDG WDNFFISKRE NRWFIQVLHK AFSDLAL HR GLPVIEANPA RTSITCIRCG HCDRNNRHGE MFLCLSCNDL RHADREIATR NLTRVAVTGE MIPRRIEPGE QSGDTKKA R SARKGKKAVI SKREAA

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unclassified sequences (unknown)
Molecular weightTheoretical: 14.652684 KDa
SequenceString:
UCAACGCUUG CUCGGUUCGC CGAGACUCCC 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: 13.012336 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC) (DA)(DA)(DG)(DA)(DA)(DG)(DT)(DC)(DG)(DT) (DC)(DG)(DT)(DG)(DC)(DA)(DT)(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: 12.852241 KDa
SequenceString:
(DT)(DG)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DC) (DT)(DC)(DC)(DC)(DC)(DA)(DT)(DG)(DC)(DA) (DC)(DG)(DA)(DC)(DG)(DA)(DC)(DT)(DT) (DC)(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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95686
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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