+Open data
-Basic information
Entry | Database: PDB / ID: 7r21 | ||||||||||||
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Title | elongated Cascade complex from type I-A CRISPR-Cas system | ||||||||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / elongated Cascade complex / cascade / type I-A / genome editing | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Hu, C. / Ni, D. / Nam, K.H. / Stahlberg, H. / Terns, M. / Ke, A. | ||||||||||||
Funding support | United States, Switzerland, 3items
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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, K.H. / Terns, M. / Stahlberg, H. / Ke, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r21.cif.gz | 744.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r21.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r21_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7r21_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7r21_validation.xml.gz | 116.6 KB | Display | |
Data in CIF | 7r21_validation.cif.gz | 184.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/7r21 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/7r21 | HTTPS FTP |
-Related structure data
Related structure data | 14244MC 7r2kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 12208.933 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0643 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q8U332 #2: Protein | Mass: 36989.148 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF0642 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q8U333 #3: Protein | | Mass: 29147.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cas5a, PFDSM3638_03200 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: A0A5C0XNV9 #4: RNA chain | | Mass: 19979.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.55 MDa / Experimental value: YES | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Buffer component | Conc.: 150 mM / Name: sodium chloride / Formula: NaCl | ||||||||||||||||||||||||||||
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: 4s force 0 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8500 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240851 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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