+Open data
-Basic information
Entry | Database: PDB / ID: 8qwd | ||||||
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Title | Apo ReChb | ||||||
Components | ReChb | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Cas / cryo-EM / ancestral sequence reconstruction / biotechnology | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å | ||||||
Authors | Lopez-Alonso, J.P. / Ubarretxena-Belandia, I. / Tascon, I. | ||||||
Funding support | 1items
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Citation | Journal: Nature Biotechnology / Year: 2024 Title: A resurrected ancestor of Cas12a expands target access and substrate 2 recognition for nucleic-acid editing and detection Authors: Jabalera, Y. / Tascon, I. / Samperio, S. / Lopez-Alonso, J.P. / Gonzalez-Lopez, M. / Aransay, A.M. / Abascal-Palacios, G. / Beisel, C.L. / Ubarretxena-Belandia, I. / Jimenez-Perez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qwd.cif.gz | 239.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qwd.ent.gz | 187.9 KB | Display | PDB format |
PDBx/mmJSON format | 8qwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qwd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8qwd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8qwd_validation.xml.gz | 47 KB | Display | |
Data in CIF | 8qwd_validation.cif.gz | 68 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/8qwd ftp://data.pdbj.org/pub/pdb/validation_reports/qw/8qwd | HTTPS FTP |
-Related structure data
Related structure data | 18691MC 8qweC 8qwfC C: citing same article (ref.) M: map data used to model this data |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 148954.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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 | Name: Apo ReChb / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Source (natural) | Organism: synthetic construct (others) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3) / Plasmid: pET-28a(+) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.1 sec. / Electron dose: 49.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 14874 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1967948 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 254316 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Details: ModelAngelo / Source name: Other / Type: other | ||||||||||||||||||||||||||||||||||||||||||||
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