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- EMDB-61266: Cryo-EM structure of the type VII CRISPR-Cas14 effector complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61266
TitleCryo-EM structure of the type VII CRISPR-Cas14 effector complex
Map data
Sample
  • Complex: The type VII CRISPR-Cas14 effector complex
    • RNA: crRNA
    • RNA: tgRNA
    • Protein or peptide: Cas5
    • Protein or peptide: Cas7
    • Protein or peptide: Cas14
  • Ligand: ZINC ION
Keywordsbeta-CASP / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Biological speciesMycobacterium phage Bxb1 (virus) / synthetic construct (others) / Spirochaetota bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsHiraizumi M / Yamashita K / Nishimasu H
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR23B6 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of type VII CRISPR-Cas14 effector complex
Authors: Hiraizumi M
History
DepositionAug 22, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61266.png

Downloads & links

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Map

FileDownload / File: emd_61266.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 360 pix.
= 398.4 Å		1.11 Å/pix.
x 360 pix.
= 398.4 Å		1.11 Å/pix.
x 360 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.14699072 - 0.40072468
Average (Standard dev.)0.000046398873 (±0.0077906316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 398.40015 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61266_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61266_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_61266_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 : The type VII CRISPR-Cas14 effector complex

EntireName: The type VII CRISPR-Cas14 effector complex
Components
  • Complex: The type VII CRISPR-Cas14 effector complex
    • RNA: crRNA
    • RNA: tgRNA
    • Protein or peptide: Cas5
    • Protein or peptide: Cas7
    • Protein or peptide: Cas14
  • Ligand: ZINC ION

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Supramolecule #1: The type VII CRISPR-Cas14 effector complex

SupramoleculeName: The type VII CRISPR-Cas14 effector complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)

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Macromolecule #1: crRNA

MacromoleculeName: crRNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.080244 KDa
SequenceString:
GGUUAAAACU AAGCUUUUUA ACAGUGGCCU UAUUAAAUGA CUUCUCGUUU AAGUCCCAUA

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Macromolecule #2: tgRNA

MacromoleculeName: tgRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 31.726975 KDa
SequenceString:
GGUUUCAGGA GCUAAGGAAG CUAAAAUGGC CGAGAAGUCA UUUAAUAAGG CCACUGUUAA AAAGCUUUCA AAAUUGGAGA AAAAAAUCA CUGGAUAUA

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Macromolecule #3: Cas5

MacromoleculeName: Cas5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Spirochaetota bacterium (bacteria)
Molecular weightTheoretical: 27.139533 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEIKGILES ITGFSIPLDN GEYALYPAGR HLRGAIGYIA FNLDLPISSK FLDFDFDDII FRDLLPISKC GKIFYPEKNS NSLKCPSCN EIYGSSVLRN IMARGLSYKE VIEGKKYRLS IIVKDEKYLN EMEAIIRYIL SYGIYLGNKV SKGYGKFKIK E YSIVDILP ...String:
MKEIKGILES ITGFSIPLDN GEYALYPAGR HLRGAIGYIA FNLDLPISSK FLDFDFDDII FRDLLPISKC GKIFYPEKNS NSLKCPSCN EIYGSSVLRN IMARGLSYKE VIEGKKYRLS IIVKDEKYLN EMEAIIRYIL SYGIYLGNKV SKGYGKFKIK E YSIVDILP VKDSEVLLLS DAIIDNGEKD IVFSKKEISS SKFEIIRKRG KAKGDIIRDN NHNGFYIGKY GGLGFGEIIS LK

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Macromolecule #4: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Spirochaetota bacterium (bacteria)
Molecular weightTheoretical: 22.255604 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAKTMKKIYV TMKTLSPLYT GEVRREDKEA AQKRVNFPVR KTATNKVLIP FKGALRSALE IMLKAKGENV CDTGESRARP CGRCVTCSL FGSMGRAGRA SVDFLISNDT KEQIVRESTH LRIERQTKSA SDTFKGEEVI EGATFTATIT ISNPQEKDLS L IQSALKFI ...String:
MAKTMKKIYV TMKTLSPLYT GEVRREDKEA AQKRVNFPVR KTATNKVLIP FKGALRSALE IMLKAKGENV CDTGESRARP CGRCVTCSL FGSMGRAGRA SVDFLISNDT KEQIVRESTH LRIERQTKSA SDTFKGEEVI EGATFTATIT ISNPQEKDLS L IQSALKFI EENGIGGWLN KGYGRVSFEV KSEDVATDRF LK

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Macromolecule #5: Cas14

MacromoleculeName: Cas14 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Spirochaetota bacterium (bacteria)
Molecular weightTheoretical: 70.579977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKFIGGASK VTGSAFLLET GNAKILIDCG IEQEKGIEKD NNEIIEKKIN EIGKADICIL THAHLDHSGL VPLLVKKRKV NKIISTPAT KELCRLLFND FQRIQEENND IPLYSYDDIE SSFEIWDEID DRNTIELFDT KITFYNNSHI IGSVSVFIET H NGNYLFSG ...String:
MIKFIGGASK VTGSAFLLET GNAKILIDCG IEQEKGIEKD NNEIIEKKIN EIGKADICIL THAHLDHSGL VPLLVKKRKV NKIISTPAT KELCRLLFND FQRIQEENND IPLYSYDDIE SSFEIWDEID DRNTIELFDT KITFYNNSHI IGSVSVFIET H NGNYLFSG DIGSKLQQLM DYPPDMPDGN VDYLILESTY GNKSHDSSDR DRLLEIAKTT CENGGKVLIP SFAIGRLQEV LY TFSNYNF NFPVYIDSPM GSKVTNLIKE YNIYLKKKLR RLSITDDLFN NKYIAINTSN QSKELSNSKE PAVIISASGM LEG GRILNH LEQIKNDENS TLIFVGYQAQ NTRGRKILDG EEKVRCRIEK LNSFSAHADQ DELIDYIERL KYTPYKVFLV HGEK EQREI LAKRIISKKI RVELPENYSQ GKEILIEKKV VLNINTDNMC NFASYRLMPF SGFIVEKDDR IEINDKNWFD MIWNE EYNK MRSQIVAEDF STDQNEDSMA LPDMSHDKII ENIEYLFNIK ILSKNRIKEF WEEFCKGQKA AIKYITQVHR KNPNTG RRN WNPPEGDFTD NEIEKLYETA YNTLLSLIKY DKNKVYNILI NFNPKL

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 13 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 74619
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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