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- EMDB-52275: Structure of Ba1Cas12a3 binary complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52275
TitleStructure of Ba1Cas12a3 binary complex
Map data
Sample
  • Complex: Ba1Cas12a3 binary complex
    • Protein or peptide: Ba1Cas12a3
    • RNA: crRNA
Keywordscrispar-cas nuclease / RNA BINDING PROTEIN
Function / homology:
Function and homology information
Biological speciesBacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria) / Bacteroidota bacterium (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYuan B / Heinz DW
Funding support Germany, 1 items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of Ba1Cas12a3 binary complex
Authors: Yuan B / Heinz DW
History
DepositionDec 5, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52275.png

Downloads & links

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Map

FileDownload / File: emd_52275.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.21079458 - 0.28643036
Average (Standard dev.)0.00038586406 (±0.006980524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 232.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52275_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_52275_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 : Ba1Cas12a3 binary complex

EntireName: Ba1Cas12a3 binary complex
Components
  • Complex: Ba1Cas12a3 binary complex
    • Protein or peptide: Ba1Cas12a3
    • RNA: crRNA

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Supramolecule #1: Ba1Cas12a3 binary complex

SupramoleculeName: Ba1Cas12a3 binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)

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Macromolecule #1: Ba1Cas12a3

MacromoleculeName: Ba1Cas12a3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroidota bacterium (bacteria)
Molecular weightTheoretical: 135.303656 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: METYKVTKTI RFKLEAQNVP EIQKDIEGLQ SEFNLANFVS DLKNYLDQVR NYLFSEGKEH VFVNNKITIK REWLQNHAKQ EWVDFLEKN KRNNSLNNHT RRIQMSIGDF TGLASKIEGT FDEINSICKG LADAAGAQAN KRTKRERTGL LLKRLQARKA L PSLFSLIE ...String:
METYKVTKTI RFKLEAQNVP EIQKDIEGLQ SEFNLANFVS DLKNYLDQVR NYLFSEGKEH VFVNNKITIK REWLQNHAKQ EWVDFLEKN KRNNSLNNHT RRIQMSIGDF TGLASKIEGT FDEINSICKG LADAAGAQAN KRTKRERTGL LLKRLQARKA L PSLFSLIE NSADKNETGN LSLQLKNKSI LIEQQLAAGV QTFLPAQSGG LPVAKASFNY YTINKKPVDF GNEKSELESR LK ISIDTIF KLTRENFSKK IEEAITADIQ KELNNGKTLL LGDVPMLGIE NYVSLRQILK NIKSNQKKAF SDLMQSGKNY NEL KATNLY LLNTIEQRQF DNYKVKTNEL EKLAVKINQA TNDNQKKELI SNKQRVAKQR GIIMRDNFAT WKSFSNFYRT ISQE HGKIL ALLKGIEKER TESQLLKYWA LILENNGQHK LILIPREKAA SCKQWIASLN PSGDKLTKLF WFESLTYRSL QKLCF GFTE NGNNKFNKNI QNLLPKDNSR KIINGEFAFQ GDEQKKIKFY QSVLESKYAQ SVLNIPIQQV QADIINQSFA SLDDFQ IAL EKICYRLFAV VEANIEAELL KNDKAQIFNI TSSDLRKEAK DKIKSHTQIW KAFWTSENKQ NNFETRLNPE ITITYRQ PK QSKIDKYGER SQKNNRYLHA QYTLITTISE HSNSPTKILS FMSDDEFKSS VDTFNKKFKK DEIKFAFGID NGEVELST L GVYFPAFDKT TYKEKVAELE KVNDYGFEVL TIRNLNYKET DYNGKERKII QNPSYFLKKE NYLRTFNKSE TAYQKMFTE QFEKKKLLTL DLTTAKVICG HIVTNGDVPA LFNLWLKHAQ RNIFEMNDHI QKETAKKIVL KNQLDTDNEK LKFAEYISKE KEFGKLNDD EKMKYTKWIF EDRDQNNFTE VENKKFKRCQ KIYGNYSTKA KAPVLFASCF IDEELQSVTD IFDVRHIFKK R EDFYALKT EEEIKQLIDS YNTNRASHDI SNEELDLKIL NTKKALVANA VGVIDFLYKH YERRLGGEGL IIKEGFGTGK VE DGIEKFS GNIYRILERK LYQKFQNYGL VPPIKSLMAV RANGIENNKN AILQLGNVGF IDPAGTSQEC PVCIEGRLEH TTT CPNKCG FNSERIMHSN DGIASFNIAK RGFNNFVKSK TDKQLEHHHH HH

UniProtKB: UNIPROTKB: A0A2N2ZXC5

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Macromolecule #2: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.859344 KDa
SequenceString:
GUCUAAACCG ACCCAAUAAU UUCUACUGUU GUAGAUGAGG GAUCUCGCUC CUGGAAGAUG GUGAU

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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: 7.5 / Details: 50mM TrisHCl 150mM NaCl 1mM DTT,5%glycerol
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99354
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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