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- EMDB-51023: Structure of the minimal type I-F2 CRISPR-Cas DNA-interference co... -

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Basic information

Entry
Database: EMDB / ID: EMD-51023
TitleStructure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.
Map data
Sample
  • Complex: Type I-F2 Cascade-Cas3 effector complex.
    • Protein or peptide: DEAD-like helicases-like protein
    • Protein or peptide: Cas5fv helical domain-containing protein
    • Protein or peptide: CRISPR-associated protein, Csy4 family
    • Protein or peptide: CRISPR-associated protein Cas7
    • RNA: RNA (61-MER)
    • DNA: DNA (39-MER)
    • DNA: DNA (41-MER)
  • Ligand: MAGNESIUM ION
KeywordsType I-F2 CRISPR system / Nuclease-Helicase Cas3 / Structural characterization / Protein-DNA-RNA complex / Cryo-EM. / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / helicase activity / endonuclease activity / defense response to virus / nucleic acid binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Cas5fv helical domain / : / : / Cas5fv helical domain / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / Cas3, HD domain / : / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily ...Cas5fv helical domain / : / : / Cas5fv helical domain / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / Cas3, HD domain / : / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DEAD-like helicases-like protein / Uncharacterized protein / Cas5fv helical domain-containing protein / CRISPR-associated protein, Csy4 family
Similarity search - Component
Biological speciesShewanella putrefaciens CN-32 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMais CN / Perry TN / Sanchez-Londono M / Steinchen W / Innis CA / Randau L / Paush P / Bange G
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)3869European Union
German Research Foundation (DFG)405858511 Germany
CitationJournal: To Be Published
Title: Structure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.
Authors: Mais CN / Perry TN / Sanchez-Londono M / Steinchen W / Randau L / Innis CA / Pausch P / Bange G
History
DepositionJul 13, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51023.png

Downloads & links

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Map

FileDownload / File: emd_51023.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å		0.93 Å/pix.
x 300 pix.
= 279. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.010042855 - 0.027498147
Average (Standard dev.)0.00004639307 (±0.0009971012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51023_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_51023_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-F2 Cascade-Cas3 effector complex.

EntireName: Type I-F2 Cascade-Cas3 effector complex.
Components
  • Complex: Type I-F2 Cascade-Cas3 effector complex.
    • Protein or peptide: DEAD-like helicases-like protein
    • Protein or peptide: Cas5fv helical domain-containing protein
    • Protein or peptide: CRISPR-associated protein, Csy4 family
    • Protein or peptide: CRISPR-associated protein Cas7
    • RNA: RNA (61-MER)
    • DNA: DNA (39-MER)
    • DNA: DNA (41-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Type I-F2 Cascade-Cas3 effector complex.

SupramoleculeName: Type I-F2 Cascade-Cas3 effector complex. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #7, #6, #1-#5
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)

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Macromolecule #1: CRISPR-associated protein, Csy4 family

MacromoleculeName: CRISPR-associated protein, Csy4 family / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 19.055926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MREAELSSKV FTKFHKALVT LNSHKIGISF PQMKLSLGQL FRIHGDASLL HDLQGLDWLG PLAGYCQVTA VSAVPDHVQY RIVSVKRSN LSKAKLKRLI ARGSIDKDGE KRYKVKMLGQ GFDNPYLDLF SSSTGQVYRK FFEFSDIQAH PLDGEFDSYG L SKTATVPW F

UniProtKB: CRISPR-associated protein, Csy4 family

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Macromolecule #2: CRISPR-associated protein Cas7

MacromoleculeName: CRISPR-associated protein Cas7 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 36.481035 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHMQK VTGIKSVDFK IKALGHGVVN WNGPTTLTGD DGKTVDNHTL PKLRGYTNLT GKVKDETGYK YKKQATDINF KETPLYISQ NCIRHHLFRE QAFDLHYASD KNLKNVLASI TGLIRGYVVP SSQCKRTSPL LLEDFVDQLG NGNFEQYGQA G ARDSTSFF ...String:
MGHHHHHMQK VTGIKSVDFK IKALGHGVVN WNGPTTLTGD DGKTVDNHTL PKLRGYTNLT GKVKDETGYK YKKQATDINF KETPLYISQ NCIRHHLFRE QAFDLHYASD KNLKNVLASI TGLIRGYVVP SSQCKRTSPL LLEDFVDQLG NGNFEQYGQA G ARDSTSFF SKTTFGDTEY ISYGSISIEQ LQFISLDKKF DRAAMVIKEG EGEVIAAELQ NYIQSLNPSL NPQAIFHSNY VR RGTIFEE GECGILLNDD AVKALVAETL ERLANLSIRQ AKGYMYVDDI TVDYNDSHKM MRIKRDESEI INEQHAPFAQ YFY AK

UniProtKB: Uncharacterized protein

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Macromolecule #6: Cas5fv helical domain-containing protein

MacromoleculeName: Cas5fv helical domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 37.904441 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIIIEYDSC WRNAFLGGSN NEPVPKKGRE FLGSMTSLKK EGNFKVCENT LDTVMGVLNR LIGDQRKLYQ ARSKMYESAY YFEALEDKV SFIDKPQLTN EISFIRNMNG STDQNAFTGM IKVSDPVFTS EYSQQFWGVL ALDFTQLCDF IIKQSQVVGS I ELNPLSII ...String:
MKIIIEYDSC WRNAFLGGSN NEPVPKKGRE FLGSMTSLKK EGNFKVCENT LDTVMGVLNR LIGDQRKLYQ ARSKMYESAY YFEALEDKV SFIDKPQLTN EISFIRNMNG STDQNAFTGM IKVSDPVFTS EYSQQFWGVL ALDFTQLCDF IIKQSQVVGS I ELNPLSII NRLESLNQEK ALENSDDLAQ VLKVLNEYFP DIEYLNNKGL ITPISIYCSA LYLQLARLET SFNMTTAKTK AG GISGISK RGFTKKDFMD RYTTGPKKTI WGNPFIKKEK IKGQGEVTSM MTKASGQLEI SIDVDRDKAQ EIKILIENAG VSS FYLGKK GLAYVSNIKL

UniProtKB: Cas5fv helical domain-containing protein

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Macromolecule #7: DEAD-like helicases-like protein

MacromoleculeName: DEAD-like helicases-like protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 99.727641 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHKP KQGVLYANTQ LQPLSEHLFA VGFVAELLHR QLFPENTQFS IANFIAGCLH DLGKIQPKFQ EWVTNPKKRD FIAEDGQHI DDAKFSFDKH PRHNEVSLLL YQLLDSTELK LLNPSNKRSV KHALYWHHAK PFRKEKNGFD TYKDISKKLV A NQKEIGLS ...String:
MGHHHHHHKP KQGVLYANTQ LQPLSEHLFA VGFVAELLHR QLFPENTQFS IANFIAGCLH DLGKIQPKFQ EWVTNPKKRD FIAEDGQHI DDAKFSFDKH PRHNEVSLLL YQLLDSTELK LLNPSNKRSV KHALYWHHAK PFRKEKNGFD TYKDISKKLV A NQKEIGLS DIVGQAQTLL RQVIGIDKKY RELTNRLLEK AFLAEVEQDL EANLPDAPAL PSYKEYEFEE SVSANSTNVK LN ALNNIVR ACLISADRTV SALSAAELHT AIFERQLEEI VTELLEVETT LSSDIDTCLN AFFPTSERSQ KQRDIAKQLT TAE DVAVLA GAAGCGKTKI ALEWAKLQGV KRIIWVCPRV QVCQGLFYEL TSEQYLPNST IEINTGEFKF HNQWDNPIPD DENF SGDIV LTTIDQILGS VISHTKANTL IDFLNVHVVF DEFHEYVNMP AFNLLFAELI AAKKMQKDQA KTLLVSATPH YVFVE DLLG IHPDDIKIMP SFNPSQYQLD FKIFDDTNLS NINPLFAQQS GCTFVISNMA LTAQNSFIVN QHNENAVLLH SKFIKS DKR KWFGEVYEAY KRDGTRKYEV LRSGPIVQAS LNISCDYMVA EITSAEDCLQ RLGRLDRFGE NSDVNTYTLA VPESIAN GK GKSPAAGFLS KMYALSSVRA WYQFLHSELA DKTFTLPEIY QLYFAFHHTE RNRGFIASDL VAALKNSVQQ INAKVVDP I TVPPKNNKDK KRTKISKGSL RGDNRFVQLA VVDLSQAEPK YIEAYAYSIP LDDDSNIDNL TYATKAICGY DQSDKDLLS HMFKKHHNIM GGTGKAFTDK ILLNEARDPE SPIYLSYTTN DLLQVGGESA RHPHAIYYAV CDKQAIGAMS IKQINQTTED EE

UniProtKB: DEAD-like helicases-like protein

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Macromolecule #3: RNA (61-MER)

MacromoleculeName: RNA (61-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 19.531744 KDa
SequenceString:
CUUAGAAAUA UCGCCCAGCA AGACGCGCAA ACCUAUAACC GUUCACCGCC GCACAGGCGG C

GENBANK: GENBANK: CP046329.1

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Macromolecule #4: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 17.248053 KDa
SequenceString: (DC)(DC)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC) (DA)(DC)(DC)(DA)(DT)(DC)(DA)(DT)(DT)(DA) (DT)(DT)(DA)(DT)(DT)(DG)(DT)(DT)(DA) (DT)(DT)(DA)(DT)(DT)(DC)(DT)(DT)(DA)(DG) (DT) (DA)(DT)(DT)(DA)(DT)(DT) ...String:
(DC)(DC)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC) (DA)(DC)(DC)(DA)(DT)(DC)(DA)(DT)(DT)(DA) (DT)(DT)(DA)(DT)(DT)(DG)(DT)(DT)(DA) (DT)(DT)(DA)(DT)(DT)(DC)(DT)(DT)(DA)(DG) (DT) (DA)(DT)(DT)(DA)(DT)(DT)(DC)(DC) (DC)(DC)(DT)(DC)(DC)(DT)(DC)(DG)(DC)

GENBANK: GENBANK: OX359285.1

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Macromolecule #5: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Molecular weightTheoretical: 17.946416 KDa
SequenceString: (DG)(DC)(DG)(DA)(DG)(DG)(DA)(DG)(DG)(DG) (DG)(DA)(DG)(DG)(DT)(DT)(DA)(DT)(DA)(DG) (DG)(DT)(DT)(DT)(DG)(DC)(DG)(DC)(DG) (DT)(DC)(DT)(DT)(DG)(DC)(DT)(DG)(DG)(DG) (DC) (DG)(DA)(DT)(DA)(DG)(DG) ...String:
(DG)(DC)(DG)(DA)(DG)(DG)(DA)(DG)(DG)(DG) (DG)(DA)(DG)(DG)(DT)(DT)(DA)(DT)(DA)(DG) (DG)(DT)(DT)(DT)(DG)(DC)(DG)(DC)(DG) (DT)(DC)(DT)(DT)(DG)(DC)(DT)(DG)(DG)(DG) (DC) (DG)(DA)(DT)(DA)(DG)(DG)(DT)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DG)(DG)

GENBANK: GENBANK: CP046329.1

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H17N2NaO4SHEPES sodium salt
200.0 mMNaClSodium chloride
20.0 mMKClPotassium chloride
20.0 mMMgCl2Magnesium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 7698 / Average exposure time: 3.7 sec. / Average electron dose: 49.773 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2463680
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5o6u


Details: Structure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 250975
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 5.0)
Final 3D classificationSoftware - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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