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- EMDB-54947: Type I-F_HNH variant Cascade target-free RNP, HNH domain in inwar... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54947
TitleType I-F_HNH variant Cascade target-free RNP, HNH domain in inwards position
Map data
Sample
  • Complex: Type I-F_HNH effector complex bound to dsDNA
    • Protein or peptide: Cas6f
    • Protein or peptide: Cas8f fusion with HNH
  • Protein or peptide: Cas5f
  • Protein or peptide: Cas7f
  • RNA: crRNA
KeywordsCRISPR-Cas Type I-F HNH nuclease / RNA BINDING PROTEIN
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / nucleic acid binding / zinc ion binding
Similarity search - Function
CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / HNH endonuclease / HNH endonuclease / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / HNH nucleases ...CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / HNH endonuclease / HNH endonuclease / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / HNH nucleases / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / HNH nuclease
Similarity search - Domain/homology
Cas5f / Cas6f / Cas7f / Cas8f fusion with HNH
Similarity search - Component
Biological speciesSelenomonas sp. (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsFuglsang A / Montoya G
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
CitationJournal: To Be Published
Title: Conformational Dynamics of CRISPR-Cas Type I-F-HNH informs Nickase Engineering in a Cascade Scaffold
Authors: Fuglsang A / Montoya G
History
DepositionAug 31, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54947.png

Downloads & links

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Map

FileDownload / File: emd_54947.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 420 pix.
= 304.5 Å		0.73 Å/pix.
x 420 pix.
= 304.5 Å		0.73 Å/pix.
x 420 pix.
= 304.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.014398512 - 2.150874
Average (Standard dev.)0.0016219907 (±0.027685903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 304.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54947_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_54947_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 : Type I-F_HNH effector complex bound to dsDNA

EntireName: Type I-F_HNH effector complex bound to dsDNA
Components
  • Complex: Type I-F_HNH effector complex bound to dsDNA
    • Protein or peptide: Cas6f
    • Protein or peptide: Cas8f fusion with HNH
  • Protein or peptide: Cas5f
  • Protein or peptide: Cas7f
  • RNA: crRNA

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Supramolecule #1: Type I-F_HNH effector complex bound to dsDNA

SupramoleculeName: Type I-F_HNH effector complex bound to dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Cas8f fusion with HNH

MacromoleculeName: Cas8f fusion with HNH / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 43.706289 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLRSKHHHHS GHHHTGHHHH SGSHHHTGGS GENLYFQGSG GLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSP GNIGAYDILS SDMNCGYLDT ANAGWKEPDI VTNDAKYKRP QGFVAMEMSD GRTVMEHLQE DSAELRHEME E LTDKYDEI ...String:
MLRSKHHHHS GHHHTGHHHH SGSHHHTGGS GENLYFQGSG GLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSP GNIGAYDILS SDMNCGYLDT ANAGWKEPDI VTNDAKYKRP QGFVAMEMSD GRTVMEHLQE DSAELRHEME E LTDKYDEI RDGILNMPSM QPYRTNQFIK QVFFPVGGSY HLLSILPSTV LNYEVSDRLY RSKIPKIRLR LLSSNAASTT GS RLVSKNK WPLVFQALPP KFLEKNLAKA LDKEYLLPDI NIDELEGVDN GCLIDEALLP LIIDEGKRKG EGNYRPRHLR DER KEETVQ AFLDKYGYCN IPVGYEVHHI VPLSQGGADS IKNMIMLSIE HHERVTEAHA SYFKWRNT

UniProtKB: Cas8f fusion with HNH

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Macromolecule #2: Cas5f

MacromoleculeName: Cas5f / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 28.703135 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMKGYILLEK VNIENANAFN NIIVGIPAIT SFLGFARALE RKLNAKEIAI RINGVGLEFH EYELKGYKNK RGQYVTSCPL PGSIPGQNE KKLDAHIMNQ AYIDLNMSFL LEVEGPHVDM STCKSIKSTM ETLRIAGGII RNYKKIRLID TLADIPYGYF L TLRQDNLN ...String:
MMKGYILLEK VNIENANAFN NIIVGIPAIT SFLGFARALE RKLNAKEIAI RINGVGLEFH EYELKGYKNK RGQYVTSCPL PGSIPGQNE KKLDAHIMNQ AYIDLNMSFL LEVEGPHVDM STCKSIKSTM ETLRIAGGII RNYKKIRLID TLADIPYGYF L TLRQDNLN DAAGDDMLDK MIHALQQEDT LVPIAVGFKA LSEVGHVEGQ RDPEKDHCFV ESIFSLGGFE CSKILEDINS CL WRYKTEE GLYLCTII

UniProtKB: Cas5f

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Macromolecule #3: Cas6f

MacromoleculeName: Cas6f / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 20.735873 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MFSQILIIKP GTGISPNIII SEDIFPVLHS LFVEHDKKFG ITFPAYSFDK KGHLGNIIEV LSEDKEALAS LCLEEHLAEV TDYVKVKKE ITFTDDYVLF KRIREENQYE TTARRMRKRG HTELGRPLEM HIKKKNQQIF CHAYIKVKSA STGQSYNIFL A PTDIKHGS FSAYGLLRGD THA

UniProtKB: Cas6f

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Macromolecule #4: Cas7f

MacromoleculeName: Cas7f / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 38.700172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECD TLRIDFGIKV LPVKESMYSC SDYNYRTAIY QKIDEYIAED GFLTLAKRYV NNIANARFLW RNRKGAEIIE T IVTIEDKE ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECD TLRIDFGIKV LPVKESMYSC SDYNYRTAIY QKIDEYIAED GFLTLAKRYV NNIANARFLW RNRKGAEIIE T IVTIEDKE YPSFNSKSFN LDTFVEDNAT INEIAQQIAD TFAGKREYLN IYVTCFVKIG CAMEVYPSQE MTFDDDDKGK KL FKFEGSA GMHSQKINNA LRTIDTWYPD YTTYEFPIPV ENYGAARSIG IPFRPDTKSF YKLIDRMILK NEDLPIEDKH YVM AILIRG GMFSKKQEK

UniProtKB: Cas7f

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Macromolecule #5: crRNA

MacromoleculeName: crRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 19.440611 KDa
SequenceString:
UUUAGAAGGA GAAGUCAUUU AAUAAGGCCA CUGUUAAAAA GUGUACCGCC GGAUAGGCGG

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 1.8 µm / Nominal defocus min: 0.6 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: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17308
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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