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- EMDB-37799: Cryo-EM mini structure of Cas12-1 with 14 nt complementary hetero... -

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Basic information

Entry
Database: EMDB / ID: EMD-37799
TitleCryo-EM mini structure of Cas12-1 with 14 nt complementary heteroduplex
Map data
Sample
  • Complex: Ternary complex of mini Cas12-1 with 14 nt complementary heteroduplex
    • Protein or peptide: Cas12-1
    • DNA: TS
    • RNA: crRNA
    • DNA: NTS
KeywordsCrispr-Cas12-1 / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesunclassified sequences (unknown)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsKuo Z / Xi Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32188102 China
CitationJournal: To Be Published
Title: Cryo-EM mini structure of Cas12-1 with 14 nt complementary heteroduplex
Authors: Kuo Z / Xi Z
History
DepositionOct 16, 2023-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37799.png

Downloads & links

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Map

FileDownload / File: emd_37799.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-0.029736448 - 1.690773
Average (Standard dev.)0.0005520666 (±0.014906558)
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_37799_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_37799_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 mini Cas12-1 with 14 nt complementary heteroduplex

EntireName: Ternary complex of mini Cas12-1 with 14 nt complementary heteroduplex
Components
  • Complex: Ternary complex of mini Cas12-1 with 14 nt complementary heteroduplex
    • Protein or peptide: Cas12-1
    • DNA: TS
    • RNA: crRNA
    • DNA: NTS

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Supramolecule #1: Ternary complex of mini Cas12-1 with 14 nt complementary heteroduplex

SupramoleculeName: Ternary complex of mini Cas12-1 with 14 nt complementary heteroduplex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: TS

MacromoleculeName: TS / type: dna / ID: 2 / 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)(DG)(DA)(DA)(DG)(DT)(DC)(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: 12.874237 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)(DG)(DA)(DC)(DT)(DT) (DC)(DT)(DT)(DG)(DC)(DA)(DA)(DG)(DG)(DG) (DC) (DA)(DG)

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Macromolecule #3: crRNA

MacromoleculeName: crRNA / type: rna / ID: 3 / 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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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147916
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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