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- EMDB-68050: BaCas12a3 ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-68050
TitleBaCas12a3 ternary complex
Map dataTernary
Sample
  • Complex: Ternay complex of crRNA and target RNA
    • Protein or peptide: Nuclease
    • RNA: RNA (43-MER)
    • RNA: RNA (27-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsCas12 / Complex / CRISPR-Cas / nuclease / IMMUNE SYSTEM/RNA / IMMUNE SYSTEM-RNA complex
Biological speciesBacteroidales (bacteria) / Bacteroidales bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsJi S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: BaCas12a3 represents a new subtype of type V CRISPR effector
Authors: Ji S
History
DepositionDec 31, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68050.png

Downloads & links

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Map

FileDownload / File: emd_68050.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTernary
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.45 Å/pix.
x 588 pix.
= 261.66 Å		0.45 Å/pix.
x 588 pix.
= 261.66 Å		0.45 Å/pix.
x 588 pix.
= 261.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.445 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.055399287 - 0.16111742
Average (Standard dev.)-0.00003139668 (±0.0037157936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 261.66 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: HalfA

Fileemd_68050_half_map_1.map
AnnotationHalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HalfB

Fileemd_68050_half_map_2.map
AnnotationHalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternay complex of crRNA and target RNA

EntireName: Ternay complex of crRNA and target RNA
Components
  • Complex: Ternay complex of crRNA and target RNA
    • Protein or peptide: Nuclease
    • RNA: RNA (43-MER)
    • RNA: RNA (27-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Ternay complex of crRNA and target RNA

SupramoleculeName: Ternay complex of crRNA and target RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacteroidales (bacteria)

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Macromolecule #1: Nuclease

MacromoleculeName: Nuclease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroidales (bacteria)
Molecular weightTheoretical: 138.106094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFIKTTKAV RFRLESNNEN TLIQESINNL NSRKEFDLNT FVDDLDAFIN DCNAFLFCSK NKGRREIFYV NPSLIVKNEW LKKYAKQDL AELKQNHTAQ RVQYKIGDID GLCYRIQDLI DDLDDIYVKL CDDASAELHE RAKRAQTALL LKRLFANNAL P CLVSLIDN ...String:
MDFIKTTKAV RFRLESNNEN TLIQESINNL NSRKEFDLNT FVDDLDAFIN DCNAFLFCSK NKGRREIFYV NPSLIVKNEW LKKYAKQDL AELKQNHTAQ RVQYKIGDID GLCYRIQDLI DDLDDIYVKL CDDASAELHE RAKRAQTALL LKRLFANNAL P CLVSLIDN TVDKNEKDNL SLKLKSLGKK LLAQLELGIQ EYLPEQSSGV NIAKASFNYY TINKKPIDYD RKIEELSDKL VT TLDFWKR DGSCNFNKSL WKLIEVKSEG KTLYLGDSPL SDTDEYASLR QILKNILAEQ KAEFSEKMQE KISYEDLTKS DLF LFNNIS KEEYNGYLEL TNQIEELATD INQEDNEYKL KKLRSDLMKL KKNRGSLINA ADRRTKEKFK TYKSFADFYR KVSQ RHGKI LAQLKGIEKE RSESQLLQYW ALMLEVNNQH KLVLIPKDKA QECKSRLESS NEQAQGTKLY WFESFTFRSL QKLCF GNLE NGSNSFYPGI RKELQYKYST EDRNGYPQFI SGEFEFKGDE QKKIQFYKDV LNTKYAQSAL SFPKEEVKRN IIEKDF ESL DDFVIALEQI CYQRYVCVNS HMINALGSYF NAQILDITSL DLRNPLNSQE KETVYAHADK KHTEIWKKFW TADNEKD NF DIRLNPEITI TYRKPKESRI AKYGVESDKY DANKKNRYLH DQLTLVTTIS EHSNSPAKNL AFTTDAELKD MIERFNAE I KKEKIKFALG IDNGEVELST LGVYLPGFKK DTKEEVFAEL KKVDEYGFKV LEIRNLRYSE NDYNGKERRI IQNPSYFMN KELYCRTFNK TAAEYDAMFA EVFEEKQLLT LDLTTAKVIN GHIVTNGDVI SLFNLWMRHA QRSIYEMNDH AIKETANDIV LKRSETLND AEKRKFIDYL NGKNKKYEDL SEREKSEYVK WVYRIWGGDY SEYGKNKAFA EISKGQRVGD YLNNVLVAVT F TGKELTNV VDIFDIRNVF KFKEDFYSLK SETEIMEEVN KYNVKNTKSI SNEELDLKLN QLKSSLVANV VGVIDFLYKQ YK ERFGGDG IIVKEGFDSA KVESDREKFS GNIYRLLERK LYQKFQNYGL VPPVKNLMLM RDVDLNDTNE FMQLGNICFV GYE GTSQNC PVCEKGRLGH TEKCSDNCGF ESKGIMHSND GIAGYNIAKR GFNNFMRKAA LEHHHHHH

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Macromolecule #2: RNA (43-MER)

MacromoleculeName: RNA (43-MER) / type: rna / ID: 2 / Details: crRNA / Number of copies: 1
Source (natural)Organism: Bacteroidales bacterium (bacteria)
Molecular weightTheoretical: 13.539866 KDa
SequenceString:
AAUUUCUACU AUUGUAGAUA AGUUUGUUCA AUUUCUUCUC UGU

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Macromolecule #3: RNA (27-MER)

MacromoleculeName: RNA (27-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Bacteroidales bacterium (bacteria)
Molecular weightTheoretical: 13.337134 KDa
SequenceString:
CAGGCAGCAA CAGAGAAGAA AUUGAACAAA CUUGAAAGUA A

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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

Concentration0.4 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 530902
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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