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- EMDB-61038: Cryo-EM structure of CasLambda2-crRNA-target DNA ternary complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-61038
TitleCryo-EM structure of CasLambda2-crRNA-target DNA ternary complex in the incompetent state
Map data
Sample
  • Complex: CasLambda2-crRNA-target DNA ternary complex
    • Protein or peptide: Cas Lambda2
    • RNA: RNA (58-MER)
    • DNA: DNA (40-MER)
    • DNA: DNA (40-MER)
  • Ligand: MAGNESIUM ION
KeywordsCRISPR-CAS12 / GENOME ENGINEERING / HYDROLASE-RNA-DNA COMPLEX / DNA BINDING PROTEIN
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsOmura SN / Hirano H / Itoh Y / Nureki O
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Structural basis for the target DNA cleavage and guide RNA processing by the CRISPR-CasLambda2
Authors: Omura SN / Hirano H / Itoh Y / Nureki O
History
DepositionAug 1, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61038.png

Downloads & links

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Map

FileDownload / File: emd_61038.map.gz / Format: CCP4 / Size: 6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 116 pix.
= 144.42 Å		1.25 Å/pix.
x 116 pix.
= 144.42 Å		1.25 Å/pix.
x 116 pix.
= 144.42 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.4198132 - 6.2985277
Average (Standard dev.)0.013762992 (±0.23123322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin626262
Dimensions116116116
Spacing116116116
CellA=B=C: 144.42 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61038_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61038_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61038_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : CasLambda2-crRNA-target DNA ternary complex

EntireName: CasLambda2-crRNA-target DNA ternary complex
Components
  • Complex: CasLambda2-crRNA-target DNA ternary complex
    • Protein or peptide: Cas Lambda2
    • RNA: RNA (58-MER)
    • DNA: DNA (40-MER)
    • DNA: DNA (40-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CasLambda2-crRNA-target DNA ternary complex

SupramoleculeName: CasLambda2-crRNA-target DNA ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: unidentified (others)

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Macromolecule #1: Cas Lambda2

MacromoleculeName: Cas Lambda2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 88.746492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHGG MKKSIKFKVK GNCPITKDVI NEYKEYYNKC SDWIKNNLTS ITIGEMAKFL QETLGKDVAY ISMGLSDEWK DKPLYHLFT KKYHTNNADN LLYYYIKEKN LDGYKGNTLN IGNTFFRQFG YFKLVVSNYR TKIRTLNCEI KRKKIDADST S EDIEMQTM ...String:
MGHHHHHHGG MKKSIKFKVK GNCPITKDVI NEYKEYYNKC SDWIKNNLTS ITIGEMAKFL QETLGKDVAY ISMGLSDEWK DKPLYHLFT KKYHTNNADN LLYYYIKEKN LDGYKGNTLN IGNTFFRQFG YFKLVVSNYR TKIRTLNCEI KRKKIDADST S EDIEMQTM YEIIKHNLNK KTDWDEFISY IENVENPNID NINRYKLLRK CFCENENMIK NKLELLSIEQ LKNFGGCIMK QH INSMTLI IQHFKIEEKE NSLGFILNLP LNKKQYQIEL WGNRQVNKGT KERDAFLNTY GENIVFIINN DELYVVFSYE YEL EKEEAN FVKTVGLDVN FKHAFFVTSE KDNCHLDGYI NLYKYLLEHD EFTNLLTNDE KKDYEELSKV VTFCPFENQL LFAR YNKMS KFCKKEQVLS KLLYALQKQL KDENRTKEYI YVSCVNKLRA KYVSYFILKE KYYEKQKEYD IEMGFVDDST ESKES MDKR RTEFPFRNTP VANELLSKLN NVQQDINGCL KNIINYIYKI FEQNGYKIVA LENLENSNFE KKQVLPTIKS LLKYHK LEN QNVNDIKASD KVKEYIENGY YELITNENNE IVDAKYTEKG AMKVKNANFF NLMMKSLHFA SVKDEFVLLS NNGKTQI AL VPSEFTSQMD STDHCLYMKK NDKGKLVKAD KKEVRTKQEK HINGLNADFN AANNIKYIVE NEVWREIFCT RPKKAEYN V PSLDTTKKGP SAILHMLKKI EAIKILETEK

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Macromolecule #2: RNA (58-MER)

MacromoleculeName: RNA (58-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 18.692006 KDa
SequenceString:
GGCUUGUUGU AUAUAUUCUU UUAUAGGUAU UAAACAACGG AGAUGAGGUG CGCGUGGC

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Macromolecule #3: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 12.591749 KDa
SequenceString:
(DT)(DG)(DT)(DC)(DT)(DA)(DT)(DT)(DT)(DA) (DG)(DG)(DA)(DG)(DA)(DT)(DG)(DA)(DG)(DG) (DT)(DG)(DC)(DG)(DC)(DG)(DT)(DG)(GS) (SC)(AS)(SC)(SC)(AS)(PST)(SC)(AS)(PST)(AS) (PST)

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Macromolecule #4: DNA (40-MER)

MacromoleculeName: DNA (40-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 12.418669 KDa
SequenceString:
(AS)(PST)(AS)(PST)(GS)(AS)(PST)(GS)(GS)(PST) (GS)(SC)(DC)(DA)(DC)(DG)(DC)(DG)(DC) (DA)(DC)(DC)(DT)(DC)(DA)(DT)(DC)(DT)(DC) (DC)(DT)(DA)(DA)(DA)(DT)(DA)(DG)(DA)(DC) (DA)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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