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- EMDB-39286: Type I-EHNH Cascade-ssDNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-39286
TitleType I-EHNH Cascade-ssDNA complex
Map data
Sample
  • Complex: Type I-EHNH Cascade-ssDNA complex
    • Protein or peptide: CRISPR system Cascade subunit CasD
    • Protein or peptide: CRISPR-associated endoribonuclease Cse3
    • RNA: 61-nt crRNA
    • Protein or peptide: CRISPR system Cascade subunit CasC
    • Protein or peptide: CRISPR-associated protein Cse1 (CRISPR_cse1)
    • Protein or peptide: CRISPR-associated protein Cse2 (CRISPR_cse2)
    • Other: DNA/RNA (47-MER)
  • Ligand: ZINC ION
Keywordsprotein / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA binding / zinc ion binding
Similarity search - Function
CRISPR-associated protein, CT1975 / CT1975-like protein / CRISPR-associated protein, CasD / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein ...CRISPR-associated protein, CT1975 / CT1975-like protein / CRISPR-associated protein, CasD / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / HNH endonuclease / HNH endonuclease / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / HNH nucleases / CRISPR-associated protein Cas5, N-terminal / HNH nuclease
Similarity search - Domain/homology
CRISPR system Cascade subunit CasC / CRISPR-associated endoribonuclease Cse3 / CRISPR system Cascade subunit CasD / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein Cse1 (CRISPR_cse1)
Similarity search - Component
Biological speciesCandidatus Cloacimonadota bacterium (bacteria) / Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Cell / Year: 2024
Title: Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems
Authors: Li Z
History
DepositionFeb 27, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39286.png

Downloads & links

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Map

FileDownload / File: emd_39286.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.040606085 - 0.07738591
Average (Standard dev.)0.0001967883 (±0.0022228733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39286_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_39286_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-EHNH Cascade-ssDNA complex

EntireName: Type I-EHNH Cascade-ssDNA complex
Components
  • Complex: Type I-EHNH Cascade-ssDNA complex
    • Protein or peptide: CRISPR system Cascade subunit CasD
    • Protein or peptide: CRISPR-associated endoribonuclease Cse3
    • RNA: 61-nt crRNA
    • Protein or peptide: CRISPR system Cascade subunit CasC
    • Protein or peptide: CRISPR-associated protein Cse1 (CRISPR_cse1)
    • Protein or peptide: CRISPR-associated protein Cse2 (CRISPR_cse2)
    • Other: DNA/RNA (47-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Type I-EHNH Cascade-ssDNA complex

SupramoleculeName: Type I-EHNH Cascade-ssDNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Candidatus Cloacimonadota bacterium (bacteria)

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Macromolecule #1: CRISPR system Cascade subunit CasD

MacromoleculeName: CRISPR system Cascade subunit CasD / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Molecular weightTheoretical: 43.621383 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSAPPNTLFL RLEGALQSWG SNEAKFALRR TADAPTKSGV LGLLCAAMGI GRAEAADSWL PKLANLRMGV RIDRPGIRWW DFHTVGAGQ RMRMAELKAP KKPSMVGAAL AETLTPSKVK TRAETLLSRR EYLADASFLV ALQGEPELVA KLSAALAKPV W AIYLGRKS ...String:
MSAPPNTLFL RLEGALQSWG SNEAKFALRR TADAPTKSGV LGLLCAAMGI GRAEAADSWL PKLANLRMGV RIDRPGIRWW DFHTVGAGQ RMRMAELKAP KKPSMVGAAL AETLTPSKVK TRAETLLSRR EYLADASFLV ALQGEPELVA KLSAALAKPV W AIYLGRKS CPPSRPVCEH PPGFYNTLEE ALSAVPLQKR WHNEPLPQIL PCVMDWIPGY DGEHAPDDAE IHYDLPVSFQ PP RHLPRFV IRRELVVGED VQVSRETGTS VWRPKGTRAD YNNSEYKKVR AERLVMDHAA CMVCKAPATT VQHVNYRRAG GKE IPEDLR ALCRLCHDAC TMLEYGSGMT TNRIDPCDPI WRERILAKRK EIVEFRSRGQ RFRKMKPEEE NG

UniProtKB: CRISPR system Cascade subunit CasD

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Macromolecule #2: CRISPR-associated endoribonuclease Cse3

MacromoleculeName: CRISPR-associated endoribonuclease Cse3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Molecular weightTheoretical: 31.218768 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIYLSRLLID TGGNPDRPRP GRKWLDNIYN VHRRLSMAFP SGLRREQDPH FLKPFSPNDF QKTPFLFRVD NNIDGNDKRA IIIVQSVLE PDWDYCFQNA LDFLAAPPET KEYNPEFKAG QLLRFRLRVN ASVRRHIPEM VQQDGQTIET GKILHKRVSL T WDASSTPD ...String:
MIYLSRLLID TGGNPDRPRP GRKWLDNIYN VHRRLSMAFP SGLRREQDPH FLKPFSPNDF QKTPFLFRVD NNIDGNDKRA IIIVQSVLE PDWDYCFQNA LDFLAAPPET KEYNPEFKAG QLLRFRLRVN ASVRRHIPEM VQQDGQTIET GKILHKRVSL T WDASSTPD QALADWLAAK SPKLGFTLQR CELLQLGWVY GSKPEPKNVK VKEQGQGYWR EHKYNPLRFR AALLEGVLEV DD PKLFLKT LSSGIGKAKS FGFGLLSVLP IRNDG

UniProtKB: CRISPR-associated endoribonuclease Cse3

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Macromolecule #4: CRISPR system Cascade subunit CasC

MacromoleculeName: CRISPR system Cascade subunit CasC / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Molecular weightTheoretical: 41.794367 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLIEIHMIQN HSPANLNRDD LGAPKTCYFG GVLRSRISSQ CIKRSIRTSN DFKALLGGVR TRRLADLIQQ EAGETECWKK AQEILNKCG FKNKDDNTKM LVFMSKDKIK DLARIVLDNS LGLTEAAQQV ANVIAQATLA PDIALCGRML EPNDKDKDKK V KWSNTTVE ...String:
MLIEIHMIQN HSPANLNRDD LGAPKTCYFG GVLRSRISSQ CIKRSIRTSN DFKALLGGVR TRRLADLIQQ EAGETECWKK AQEILNKCG FKNKDDNTKM LVFMSKDKIK DLARIVLDNS LGLTEAAQQV ANVIAQATLA PDIALCGRML EPNDKDKDKK V KWSNTTVE AALQVAHAIS THIARPEIDY FVAADDVPGE DAGAGHIGES MFASACFYKY FSIDWEQLVK NLKGDTNLAA HT VGAFLLA AAKTNPSGKQ NSFAAHNYPD GILVEFKNSP ISYANAFVRP VSVVKESDLV EQSIGQLSNY VNDIRLGYYD EQS PVIGFW FSPNNRYPLG YKHSKLASRN IGNLNELVGA VLDYIGGFKW EEVQKSKAYI GG

UniProtKB: CRISPR system Cascade subunit CasC

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Macromolecule #5: CRISPR-associated protein Cse1 (CRISPR_cse1)

MacromoleculeName: CRISPR-associated protein Cse1 (CRISPR_cse1) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Molecular weightTheoretical: 60.665359 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MYCAAVCFPQ TKYQQRGTAL KKPLVGLRKM GVEAAAWNTL KVTRDRPKLT FPDLITPQSK FLDNDLWLKY KVPIEQKEHV MYNLLCDNW VNVVYLSGKP DRISLVQTLK DAHCLQLAYS NPMDRFTVFR FLLALGYWCF ANTNVEPEPD KPLPVSWIPW L EENKEYFE ...String:
MYCAAVCFPQ TKYQQRGTAL KKPLVGLRKM GVEAAAWNTL KVTRDRPKLT FPDLITPQSK FLDNDLWLKY KVPIEQKEHV MYNLLCDNW VNVVYLSGKP DRISLVQTLK DAHCLQLAYS NPMDRFTVFR FLLALGYWCF ANTNVEPEPD KPLPVSWIPW L EENKEYFE LFGDGKRFFQ ADPSSRIRAI TDLIHEIPTA HNLCHFKHVT DYIDGLCEAC CIKGLLRLPV FTTVGGRGIG AG INNTPPF YLLWHANDLA GMLAQNWQPW DNMGIPAWLG SFQKESREVG LLAGMTWLPR KVYLHDPVPG QAACCSCGLP SEA LVYSCS IEVEPVPKGL EWKDPHGVYT DQGKSLQSKI KLMSNDRYTF ADRDWYSPLF SYLHAEGNSR QGKLWLVGFA SDKA KSIDI WDKIIELEGT DTNDELLAQL ANRATALNAM RKKPLRGDFK KSVGTPQIAD IIPHAENRIA INAGKMTENR GYSWQ DADT EYGELLTKVA YSLEPAQTVD ARLKRGNFIS RKPWPIIPES KTKPAEGDQN E

UniProtKB: CRISPR-associated protein Cse1 (CRISPR_cse1)

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Macromolecule #6: CRISPR-associated protein Cse2 (CRISPR_cse2)

MacromoleculeName: CRISPR-associated protein Cse2 (CRISPR_cse2) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Cloacimonetes bacterium ADurb.Bin088 (bacteria)
Molecular weightTheoretical: 20.300639 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MNRGTVDFIA SLENLKEGDL GILRKLRGAR LDEKLPGFDL FSALWWPLRQ KNQRAPKREV AWLIAKLFAE FRFEQREGAT LPILMGGIC RKLEPKKELP RVLARFDQLA SLDIMQMEEP LSVIMGILRK HQQVCLDWVG LTDVLSFWEQ EPVKREWSDS F IKAYKINK EDSDVD

UniProtKB: CRISPR-associated protein Cse2 (CRISPR_cse2)

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Macromolecule #3: 61-nt crRNA

MacromoleculeName: 61-nt crRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Candidatus Cloacimonadota bacterium (bacteria)
Molecular weightTheoretical: 19.681744 KDa
SequenceString:
GUGAACCGGA GAAGUCAUUU AAUAAGGCCA CUGUUAAAAA GUAUUCCCCA CGCAUGUGGG G

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Macromolecule #7: DNA/RNA (47-MER)

MacromoleculeName: DNA/RNA (47-MER) / type: other / ID: 7 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Candidatus Cloacimonadota bacterium (bacteria)
Molecular weightTheoretical: 17.561996 KDa
SequenceString:
A(DT)(DT)(DA)(DC)(DG)(DC)(DC)(DA)(DA) (DG)(DC)(DT)(DT)(DT)(DT)(DT)AAC AG(DT)GGCC (DT)(DT) A(DT)(DT)AAA(DT)GAC (DT)(DT)C(DT)CC(DT)CC(DT) (DT)GA(DT)AGA
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63162
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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