+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39167 | |||||||||
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Title | Type I-FHNH Cascade-dsDNA intermediate complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | protein / RNA / RNA BINDING PROTEIN/DNA/RNA / RNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Biological species | Selenomonas sp. (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Li Z | |||||||||
Funding support | 1 items
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Citation | Journal: Mol.Cell / Year: 2024 Title: Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems Authors: Li Z | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39167.map.gz | 98.2 MB | EMDB map data format | |
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Header (meta data) | emd-39167-v30.xml emd-39167.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39167_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_39167.png | 104.1 KB | ||
Filedesc metadata | emd-39167.cif.gz | 6 KB | ||
Others | emd_39167_half_map_1.map.gz emd_39167_half_map_2.map.gz | 98.5 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39167 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39167 | HTTPS FTP |
-Validation report
Summary document | emd_39167_validation.pdf.gz | 977.7 KB | Display | EMDB validaton report |
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Full document | emd_39167_full_validation.pdf.gz | 977.3 KB | Display | |
Data in XML | emd_39167_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_39167_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39167 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39167 | HTTPS FTP |
-Related structure data
Related structure data | 8ydbMC 8yb6C 8yeoC 8yh9C 8yhaC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_39167.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_39167_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39167_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type I-FHNH Cascade-dsDNA intermediate complex
Entire | Name: Type I-FHNH Cascade-dsDNA intermediate complex |
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Components |
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-Supramolecule #1: Type I-FHNH Cascade-dsDNA intermediate complex
Supramolecule | Name: Type I-FHNH Cascade-dsDNA intermediate complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
-Macromolecule #1: Cas5f
Macromolecule | Name: Cas5f / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 28.703135 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: Cas6f
Macromolecule | Name: Cas6f / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 20.735873 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MFSQILIIKP GTGISPNIII SEDIFPVLHS LFVEHDKKFG ITFPAYSFDK KGHLGNIIEV LSEDKEALAS LCLEEHLAEV TDYVKVKKE ITFTDDYVLF KRIREENQYE TTARRMRKRG HTELGRPLEM HIKKKNQQIF CHAYIKVKSA STGQSYNIFL A PTDIKHGS FSAYGLLRGD THA |
-Macromolecule #4: Cas7f
Macromolecule | Name: Cas7f / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 38.700172 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #5: Cas8f fusion with HNH
Macromolecule | Name: Cas8f fusion with HNH / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 39.339742 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRP QGFVAMEMSD GRTVMEHLQE DSAELRHEME ELTDKYDEIR DGILNMPSMQ PYRTNQFIKQ VFFPVGGSYH L LSILPSTV ...String: MLRNKILAAI SQKIPEEQKI NKYIEGLFQS IDKNHLATHV AKFTETNSPG NIGAYDILSS DMNCGYLDTA NAGWKEPDIV TNDAKYKRP QGFVAMEMSD GRTVMEHLQE DSAELRHEME ELTDKYDEIR DGILNMPSMQ PYRTNQFIKQ VFFPVGGSYH L LSILPSTV LNYEVSDRLY RSKIPKIRLR LLSSNAASTT GSRLVSKNKW PLVFQALPPK FLEKNLAKAL DKEYLLPDIN ID ELEGVDN GCLIDEALLP LIIDEGKRKG EGNYRPRHLR DERKEETVQA FLDKYGYCNI PVGYEVHHIV PLSQGGADSI KNM IMLSIE HHERVTEAHA SYFKWRNT |
-Macromolecule #3: 60-nt crRNA
Macromolecule | Name: 60-nt crRNA / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 19.440611 KDa |
Sequence | String: UUUAGAAGGA GAAGUCAUUU AAUAAGGCCA CUGUUAAAAA GUGUACCGCC GGAUAGGCGG |
-Macromolecule #6: TS
Macromolecule | Name: TS / type: other / ID: 6 / Number of copies: 1 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 10.086293 KDa |
Sequence | String: (DG)(DT)GGCC(DT)(DT)A(DT) (DT)AAA(DT)GAC(DT)(DT) C(DT)CCGC(DT)AA(DT) AC |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Macromolecule #7: NTS
Macromolecule | Name: NTS / type: other / ID: 7 / Number of copies: 1 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: Selenomonas sp. (bacteria) |
Molecular weight | Theoretical: 3.541243 KDa |
Sequence | String: G(DT)A(DT)(DT)AGCGG A |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |