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- EMDB-35595: Cryo-EM structure of Cas12j-SF05-crRNA-dsDNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-35595
TitleCryo-EM structure of Cas12j-SF05-crRNA-dsDNA complex
Map data
Sample
  • Complex: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA
    • Protein or peptide: Cas12j-SF05
    • RNA: crRNA
    • DNA: TS-DNA
    • DNA: NTS-DNA
KeywordsCRISPR / RNA BINDING PROTEIN-RNA complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Biological speciesBiggievirus Mos11
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang X / Duan ZQ / Zhu JK
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Discov / Year: 2023
Title: Molecular basis for DNA cleavage by the hypercompact Cas12j-SF05.
Authors: Zhiqiang Duan / Xi Zhang / Jun-Tao Zhang / Shanshan Li / Ruiheng Liu / Jie Sun / Qingzhi Zhao / Nannan Jia / Ning Jia / Jian-Kang Zhu /
History
DepositionMar 9, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35595.png

Downloads & links

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Map

FileDownload / File: emd_35595.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: 0.1
Minimum - Maximum-0.43806985 - 0.76900727
Average (Standard dev.)0.00003183102 (±0.013728838)
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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Mask #1

Fileemd_35595_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35595_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_35595_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 Cas12j-SF05 with crRNA and target dsDNA

EntireName: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA
Components
  • Complex: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA
    • Protein or peptide: Cas12j-SF05
    • RNA: crRNA
    • DNA: TS-DNA
    • DNA: NTS-DNA

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Supramolecule #1: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA

SupramoleculeName: Ternary complex of Cas12j-SF05 with crRNA and target dsDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Biggievirus Mos11

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Macromolecule #1: Cas12j-SF05

MacromoleculeName: Cas12j-SF05 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Biggievirus Mos11
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: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Biggievirus Mos11
Molecular weightTheoretical: 18.179771 KDa
SequenceString:
GCCGUCAACG UUCAACGCUU GCUCGGUUCG CCGAGACUCC CCUACGUGCU GCUGAAG

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Macromolecule #3: TS-DNA

MacromoleculeName: TS-DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Biggievirus Mos11
Molecular weightTheoretical: 16.99491 KDa
SequenceString: (DG)(DA)(DA)(DT)(DT)(DG)(DA)(DA)(DG)(DC) (DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC)(DA) (DA)(DC)(DT)(DT)(DC)(DA)(DG)(DC)(DA) (DG)(DC)(DA)(DC)(DG)(DT)(DA)(DG)(DG)(DG) (DG) (DA)(DG)(DA)(DA)(DT)(DT) ...String:
(DG)(DA)(DA)(DT)(DT)(DG)(DA)(DA)(DG)(DC) (DT)(DG)(DC)(DC)(DC)(DT)(DT)(DG)(DC)(DA) (DA)(DC)(DT)(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)(DC)(DA)(DC)(DA)

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Macromolecule #4: NTS-DNA

MacromoleculeName: NTS-DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Biggievirus Mos11
Molecular weightTheoretical: 16.900799 KDa
SequenceString: (DT)(DG)(DT)(DG)(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)(DA)(DG)(DT)(DT)(DG)(DC)(DA) (DA) (DG)(DG)(DG)(DC)(DA)(DG) ...String:
(DT)(DG)(DT)(DG)(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)(DA)(DG)(DT)(DT)(DG)(DC)(DA) (DA) (DG)(DG)(DG)(DC)(DA)(DG)(DC)(DT) (DT)(DC)(DA)(DA)(DT)(DT)(DC)

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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: 2.5 µm / Nominal defocus min: 1.0 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59719
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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