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- EMDB-67552: Cryo-EM structure of type VII CRISPR-Cas complex at the target en... -

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Basic information

Entry
Database: EMDB / ID: EMD-67552
TitleCryo-EM structure of type VII CRISPR-Cas complex at the target engagement state
Map data
Sample
  • Complex: Cryo-EM structure of type VII CRISPR-Cas complex at the target engagement state
    • Protein or peptide: a protein
    • Protein or peptide: a protein
    • Protein or peptide: a protein
    • RNA: RNA (54-MER)
    • RNA: RNA (60-MER)
  • Ligand: ZINC ION
Keywordsa protein complex / ANTIVIRAL PROTEIN/RNA / ANTIVIRAL PROTEIN-RNA complex
Biological speciesmetagenome (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang H / Zhang S
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Allosteric activation mechanism of the type VII CRISPR-Cas system.
Authors: Shuqin Zhang / Yingcan Liu / Wenqi Wu / Zhikun Liu / Qiuqiu He / Tongyao Wang / Jie Yang / Hang Yin / Zhiyong Yuan / Heng Zhang /
Abstract: Type VII CRISPR-Cas system, evolutionarily associated with type III systems, utilizes a Cascade complex formed by Cas5 and catalytically inactive Cas7 copies for target RNA binding, but instead ...Type VII CRISPR-Cas system, evolutionarily associated with type III systems, utilizes a Cascade complex formed by Cas5 and catalytically inactive Cas7 copies for target RNA binding, but instead incorporates a specialized Cas14 ribonuclease for target cleavage. Here, we report a high-quality cryo-EM structure at the target engagement state with a shortened crRNA and elucidate how the recruited Cas14 captures the target RNA and undergoes target-mediated activation. The signature Cas14 is homologous to eukaryotic CPSF73 and prokaryotic RNase J, comprising two conserved subdomains, MβL and β-CASP. Different from canonical type III systems, 5'-end target RNA, rather than 3'-end, is bent into the positively charged binding channel formed by the two subdomains to access the conserved catalytic pocket on Cas14. Two special structural features, α1 helix from Cas7 and α10 helix from Cas14, promote the bent target RNA docking into the catalytic pocket of Cas14 nuclease in concert. A dual-functional loop, displaced by the entering target RNA, induces a closed-to-open transition between the two subdomains for nuclease activation. More importantly, the flipped dual-functional loop also maintains the stabilization of incoming target RNA. Altogether, our work provides a more comprehensive understanding of type VII system mechanism, laying a mechanistic foundation for RNA-targeting tool development.
History
DepositionDec 6, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67552.png

Downloads & links

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Map

FileDownload / File: emd_67552.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 416 pix.
= 395.2 Å		0.95 Å/pix.
x 416 pix.
= 395.2 Å		0.95 Å/pix.
x 416 pix.
= 395.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.26232597 - 0.7124219
Average (Standard dev.)0.00006780791 (±0.015657535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 395.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67552_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_67552_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 : Cryo-EM structure of type VII CRISPR-Cas complex at the target en...

EntireName: Cryo-EM structure of type VII CRISPR-Cas complex at the target engagement state
Components
  • Complex: Cryo-EM structure of type VII CRISPR-Cas complex at the target engagement state
    • Protein or peptide: a protein
    • Protein or peptide: a protein
    • Protein or peptide: a protein
    • RNA: RNA (54-MER)
    • RNA: RNA (60-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of type VII CRISPR-Cas complex at the target en...

SupramoleculeName: Cryo-EM structure of type VII CRISPR-Cas complex at the target engagement state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2, #4-#5
Source (natural)Organism: metagenome (others)

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Macromolecule #1: a protein

MacromoleculeName: a protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
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 #2: a protein

MacromoleculeName: a protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
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 #3: a protein

MacromoleculeName: a protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 70.468898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKFIGGASK VTGSAFLLET GNAKILIDCG IEQEKGIEKD NNEIIEKKIN EIGKADICIL THAHLAASGL VPLLVKKRKV NKIISTPAT KELCRLLFND FQRIQEENND IPLYSYDDIE SSFEIWDEID DRNTIELFDT KITFYNNSHI IGSVSVFIET H NGNYLFSG ...String:
MIKFIGGASK VTGSAFLLET GNAKILIDCG IEQEKGIEKD NNEIIEKKIN EIGKADICIL THAHLAASGL 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 #4: RNA (54-MER)

MacromoleculeName: RNA (54-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 17.270176 KDa
SequenceString:
GGUUAAAACU CUUCUCAUGC UGGAUUCGAA AUUAGUUUAA GUCCCAUAUG GUGG

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Macromolecule #5: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: metagenome (others)
Molecular weightTheoretical: 19.354707 KDa
SequenceString:
GAACAGAAGA ACACCCAAUA GCGAAGCGCA CCUAAUUUCG AAUCCAGCAU GAGAAGCUAA

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 9 / 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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65006
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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