+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14244 | ||||||||||||
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Title | elongated Cascade complex from type I-A CRISPR-Cas system | ||||||||||||
Map data | pao-elongate | ||||||||||||
Sample |
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Keywords | elongated Cascade complex / cascade / type I-A / genome editing / ANTIVIRAL PROTEIN | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) / Escherichia coli (E. coli) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Hu C / Ni D | ||||||||||||
Funding support | United States, Switzerland, 3 items
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Citation | Journal: To Be Published Title: Structural snapshots for an atypic type I CRISPR-Cas system Authors: Ni D / Hu C / Nam KH / Terns M / Stahlberg H / Ke A | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14244.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-14244-v30.xml emd-14244.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14244_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_14244.png | 120.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14244 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14244 | HTTPS FTP |
-Validation report
Summary document | emd_14244_validation.pdf.gz | 594.6 KB | Display | EMDB validaton report |
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Full document | emd_14244_full_validation.pdf.gz | 594.1 KB | Display | |
Data in XML | emd_14244_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | emd_14244_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14244 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14244 | HTTPS FTP |
-Related structure data
Related structure data | 7r21MC 7r2kC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14244.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | pao-elongate | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.3667 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : elongated Cascade complex from Pyrococcus furiosus type I-A CRISP...
Entire | Name: elongated Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system |
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Components |
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-Supramolecule #1: elongated Cascade complex from Pyrococcus furiosus type I-A CRISP...
Supramolecule | Name: elongated Cascade complex from Pyrococcus furiosus type I-A CRISPR/Cas system type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cascade alone |
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Molecular weight | Theoretical: 550 KDa |
-Supramolecule #2: Cas11a, Cas7a and Type I-A CRISPR-associated protein Cas5
Supramolecule | Name: Cas11a, Cas7a and Type I-A CRISPR-associated protein Cas5 type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Pyrococcus furiosus DSM 3638 (archaea) |
-Supramolecule #3: CrRNA (62-MER)
Supramolecule | Name: CrRNA (62-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Cas11a
Macromolecule | Name: Cas11a / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 |
Molecular weight | Theoretical: 12.208933 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GGWIRNIGRY LSYLVDDTFE EYAYDVVDGI AKARTQEELL EGVYKALRLA PKLKKKAESK GCPPPRIPSP EDIEALEEKV EQLSNPKDL RKLAVSLALW AFASWNNCP UniProtKB: Uncharacterized protein |
-Macromolecule #2: Cas7a
Macromolecule | Name: Cas7a / type: protein_or_peptide / ID: 2 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 |
Molecular weight | Theoretical: 36.989148 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MYVRISGRIR LNAHSLNAQG GGGTNYIEIT KTKVTVRTEN GWTVVEVPAI TGNMLKHWHF VGFVDYFKTT PYGVNLTERA LRYNGTRFG QGETTATKAN GATVQLNDEA TIIKELADAD VHGFLAPKTG RRRVSLVKAS FILPTEDFIK EVEGERLITA I KHNRVDVD ...String: MYVRISGRIR LNAHSLNAQG GGGTNYIEIT KTKVTVRTEN GWTVVEVPAI TGNMLKHWHF VGFVDYFKTT PYGVNLTERA LRYNGTRFG QGETTATKAN GATVQLNDEA TIIKELADAD VHGFLAPKTG RRRVSLVKAS FILPTEDFIK EVEGERLITA I KHNRVDVD EKGAIGSSKE GTAQMLFSRE YATGLYGFSI VLDLGLVGIP QGLPVKFEEN QPRPNIVIDP NERKARIESA LK ALIPMLS GYIGANLARS FPVFKVEELV AIASEGPIPA LVHGFYEDYI EANRSIIKNA RALGFNIEVF TYNVDLGEDI EAT KVSSVE ELVANLVKMV UniProtKB: Type I-A CRISPR-associated protein Cas7/Csa2 |
-Macromolecule #3: Type I-A CRISPR-associated protein Cas5
Macromolecule | Name: Type I-A CRISPR-associated protein Cas5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 |
Molecular weight | Theoretical: 29.147219 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDILLVCLRF PFFSVAKRSY QVRTSFLLPP PSALKGALAK GLILLKPEKY ASSSLDEAAL KAIKEIESKL VDIKAVSVAP LSPLIRNAF LLKRLRNLES GSNAEKSDAM RREYTFTREL LVAYIFKNLT QEEKNLYLKA AMLIDVIGDT ESLATPVWAS F VKPEDKKA ...String: MDILLVCLRF PFFSVAKRSY QVRTSFLLPP PSALKGALAK GLILLKPEKY ASSSLDEAAL KAIKEIESKL VDIKAVSVAP LSPLIRNAF LLKRLRNLES GSNAEKSDAM RREYTFTREL LVAYIFKNLT QEEKNLYLKA AMLIDVIGDT ESLATPVWAS F VKPEDKKA PLAFSAPYTE IYSLLSSKIQ AKGKIRMYIE KMRVSPEYSK TKGPQEEIFY LPIEERRYKR IVYYARIYPP EV EKALTVD GEVLGIWIP UniProtKB: Type I-A CRISPR-associated protein Cas5 |
-Macromolecule #4: CrRNA (62-MER)
Macromolecule | Name: CrRNA (62-MER) / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 19.97984 KDa |
Sequence | String: AUUGAAAGUU GUAGUAUGCG GUCCUUGCGG CUGAGAGCAC UUCAGGAGUU GCCCGCGCCA GC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 4s force 0. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 8500 / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7r21: |