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- EMDB-54949: Type I-F_HNH variant Cascade RNP bound to dsDNA with trace of tar... -

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Basic information

Entry
Database: EMDB / ID: EMD-54949
TitleType I-F_HNH variant Cascade RNP bound to dsDNA with trace of target strand into HNH domain rotated in middle position
Map data
Sample
  • Complex: Type I-F_HNH effector complex bound to dsDNA
    • Protein or peptide: x 9 types
    • RNA: x 1 types
    • DNA: x 2 types
KeywordsCRISPR-Cas Type I-F HNH nuclease / RNA BINDING PROTEIN
Biological speciesSelenomonas sp. (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 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_54949.png

Downloads & links

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Map

FileDownload / File: emd_54949.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: 0.05
Minimum - Maximum-0.016044661 - 2.2482975
Average (Standard dev.)0.0018591764 (±0.029984675)
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: #1

Fileemd_54949_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54949_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: Cas8-HNH
    • Protein or peptide: Cas7
    • Protein or peptide: Cas7
    • Protein or peptide: Cas7
    • Protein or peptide: Cas7
    • Protein or peptide: Cas7
    • Protein or peptide: Cas7
    • Protein or peptide: Cas8-HNH
    • Protein or peptide: Cas8-HNH
    • RNA: crRNA
    • DNA: Target strand
    • DNA: Non-target strand

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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: all
Source (natural)Organism: Selenomonas sp. (bacteria)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Cas8-HNH

MacromoleculeName: Cas8-HNH / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRPQ GFVAMEMSDG RTVMEHLQED SAELRHEMEE LTDKYDEIRD GILNMPSMQP YRTNQFIKQV FFPVGGSYHL LSILPSTVLN ...String:
MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRPQ GFVAMEMSDG RTVMEHLQED SAELRHEMEE LTDKYDEIRD GILNMPSMQP YRTNQFIKQV FFPVGGSYHL LSILPSTVLN YEVSDRLYRS KIPKIRLRLL SSNAASTTGS RLVSKNKWPL VFQALPPKFL EKNLAKALDK EYLLPDINID ELEGVDNGCL IDEALLPLII DEGKRKGEGN YRPRHLRDER KEETVQAFLD KYGYCNIPVG YEVHHIVPLS QGGADSIKNM IMLSIEHHER VTEAHASYFK WRNT

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Macromolecule #2: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP SFNSKSFNLD TFVEDNATIN EIAQQIADTF AGKREYLNIY VTCFVKIGCA MEVYPSQEMT FDDDDKGKKL FKFEGSAGMH SQKINNALRT IDTWYPDYTT YEFPIPVENY GAARSIGIPF RPDTKSFYKL IDRMILKNED LPIEDKHYVM AILIRGGMFS KKQEK

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Macromolecule #3: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP SFNSKSFNLD TFVEDNATIN EIAQQIADTF AGKREYLNIY VTCFVKIGCA MEVYPSQEMT FDDDDKGKKL FKFEGSAGMH SQKINNALRT IDTWYPDYTT YEFPIPVENY GAARSIGIPF RPDTKSFYKL IDRMILKNED LPIEDKHYVM AILIRGGMFS KKQEK

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Macromolecule #4: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP SFNSKSFNLD TFVEDNATIN EIAQQIADTF AGKREYLNIY VTCFVKIGCA MEVYPSQEMT FDDDDKGKKL FKFEGSAGMH SQKINNALRT IDTWYPDYTT YEFPIPVENY GAARSIGIPF RPDTKSFYKL IDRMILKNED LPIEDKHYVM AILIRGGMFS KKQEK

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Macromolecule #5: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP SFNSKSFNLD TFVEDNATIN EIAQQIADTF AGKREYLNIY VTCFVKIGCA MEVYPSQEMT FDDDDKGKKL FKFEGSAGMH SQKINNALRT IDTWYPDYTT YEFPIPVENY GAARSIGIPF RPDTKSFYKL IDRMILKNED LPIEDKHYVM AILIRGGMFS KKQEK

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Macromolecule #6: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP SFNSKSFNLD TFVEDNATIN EIAQQIADTF AGKREYLNIY VTCFVKIGCA MEVYPSQEMT FDDDDKGKKL FKFEGSAGMH SQKINNALRT IDTWYPDYTT YEFPIPVENY GAARSIGIPF RPDTKSFYKL IDRMILKNED LPIEDKHYVM AILIRGGMFS KKQEK

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Macromolecule #7: Cas7

MacromoleculeName: Cas7 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP ...String:
MAANKKATNV TLKSRPENLS FARCLNTTEA KFWQTDFLKR HTFKLPLLIT DKAVLASKGH EMPPDKLEKE IMDPNPQKSQ SCTLSTECDT LRIDFGIKVL PVKESMYSCS DYNYRTAIYQ KIDEYIAEDG FLTLAKRYVN NIANARFLWR NRKGAEIIET IVTIEDKEYP SFNSKSFNLD TFVEDNATIN EIAQQIADTF AGKREYLNIY VTCFVKIGCA MEVYPSQEMT FDDDDKGKKL FKFEGSAGMH SQKINNALRT IDTWYPDYTT YEFPIPVENY GAARSIGIPF RPDTKSFYKL IDRMILKNED LPIEDKHYVM AILIRGGMFS KKQEK

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Macromolecule #8: Cas8-HNH

MacromoleculeName: Cas8-HNH / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRPQ GFVAMEMSDG RTVMEHLQED SAELRHEMEE LTDKYDEIRD GILNMPSMQP YRTNQFIKQV FFPVGGSYHL LSILPSTVLN ...String:
MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRPQ GFVAMEMSDG RTVMEHLQED SAELRHEMEE LTDKYDEIRD GILNMPSMQP YRTNQFIKQV FFPVGGSYHL LSILPSTVLN YEVSDRLYRS KIPKIRLRLL SSNAASTTGS RLVSKNKWPL VFQALPPKFL EKNLAKALDK EYLLPDINID ELEGVDNGCL IDEALLPLII DEGKRKGEGN YRPRHLRDER KEETVQAFLD KYGYCNIPVG YEVHHIVPLS QGGADSIKNM IMLSIEHHER VTEAHASYFK WRNT

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Macromolecule #9: Cas8-HNH

MacromoleculeName: Cas8-HNH / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Selenomonas sp. (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRPQ GFVAMEMSDG RTVMEHLQED SAELRHEMEE LTDKYDEIRD GILNMPSMQP YRTNQFIKQV FFPVGGSYHL LSILPSTVLN ...String:
MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRPQ GFVAMEMSDG RTVMEHLQED SAELRHEMEE LTDKYDEIRD GILNMPSMQP YRTNQFIKQV FFPVGGSYHL LSILPSTVLN YEVSDRLYRS KIPKIRLRLL SSNAASTTGS RLVSKNKWPL VFQALPPKFL EKNLAKALDK EYLLPDINID ELEGVDNGCL IDEALLPLII DEGKRKGEGN YRPRHLRDER KEETVQAFLD KYGYCNIPVG YEVHHIVPLS QGGADSIKNM IMLSIEHHER VTEAHASYFK WRNT

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Macromolecule #10: crRNA

MacromoleculeName: crRNA / type: rna / ID: 10
Source (natural)Organism: Selenomonas sp. (bacteria)
SequenceString:
uuuagaagga gaagucauuu aauaaggcca cuguuaaaaa guguaccgcc ggauaggcgg

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Macromolecule #11: Target strand

MacromoleculeName: Target strand / type: dna / ID: 11 / Classification: DNA
Source (natural)Organism: Selenomonas sp. (bacteria)
SequenceString:
gtacggTTTT TAACAGTGGC CTTATTAAAT GACTTCTCcg cttttt

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Macromolecule #12: Non-target strand

MacromoleculeName: Non-target strand / type: dna / ID: 12 / Classification: DNA
Source (natural)Organism: Selenomonas sp. (bacteria)
SequenceString:
aaaaagcgGA GAAGTCATTT AATAAGGCCA CTGTTAAAAA ccgtac

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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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8722
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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