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- EMDB-54919: Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in middle... -

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Basic information

Entry
Database: EMDB / ID: EMD-54919
TitleType I-F_HNH variant Cascade bound to dsDNA, HNH domain in middle position
Map data
Sample
  • Complex: Type I-F_HNH effector complex bound to dsDNA
    • Protein or peptide: Cas8f fusion with HNH
    • Protein or peptide: Cas7f
  • Protein or peptide: Cas5f
  • Protein or peptide: Cas6f
  • DNA: Non-target strand
  • DNA: Target strand
  • RNA: crRNA
  • Ligand: MAGNESIUM ION
  • Ligand: water
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: 2.4 Å
AuthorsFuglsang A / Montoya G
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 28, 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_54919.png

Downloads & links

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Map

FileDownload / File: emd_54919.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: 0.06
Minimum - Maximum-0.02802155 - 1.9826263
Average (Standard dev.)0.0018388407 (±0.029094335)
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_54919_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_54919_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: Cas8f fusion with HNH
    • Protein or peptide: Cas7f
  • Protein or peptide: Cas5f
  • Protein or peptide: Cas6f
  • DNA: Non-target strand
  • DNA: Target strand
  • RNA: crRNA
  • Ligand: MAGNESIUM ION
  • Ligand: water

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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: Cas7f

MacromoleculeName: Cas7f / type: protein_or_peptide / ID: 1 / 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 #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: Cas8f fusion with HNH

MacromoleculeName: Cas8f fusion with HNH / type: protein_or_peptide / ID: 3 / 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 #4: Cas6f

MacromoleculeName: Cas6f / type: protein_or_peptide / ID: 4 / 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 #5: Non-target strand

MacromoleculeName: Non-target strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 14.233219 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DG)(DC)(DG)(DG)(DA) (DG)(DA)(DA)(DG)(DT)(DC)(DA)(DT)(DT)(DT) (DA)(DA)(DT)(DA)(DA)(DG)(DG)(DC)(DC) (DA)(DC)(DT)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DA) (DC)(DC)(DG)(DT)(DA)(DC)

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Macromolecule #6: Target strand

MacromoleculeName: Target strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 14.062044 KDa
SequenceString:
(DG)(DT)(DA)(DC)(DA)(DA)(DT)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DA)(DG)(DT)(DG)(DG)(DC) (DC)(DT)(DT)(DA)(DT)(DT)(DA)(DA)(DA) (DT)(DG)(DA)(DC)(DT)(DT)(DC)(DT)(DC)(DC) (DG) (DC)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #7: crRNA

MacromoleculeName: crRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 19.502576 KDa
SequenceString:
UUUAGAAGGA GAAGUCAUUU AAUAAGGCCA CUGUUAAAAA GUGUACCGCC GGAUAGGCG(23G)

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 174646
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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