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Yorodumi- PDB-8utm: CryoEM Structure of Allosterically Switchable De Novo Protein sr3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8utm | ||||||
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Title | CryoEM Structure of Allosterically Switchable De Novo Protein sr322, In Closed State without Effector Peptide, off Target Multimeric State | ||||||
Components | de novo protein sr322 | ||||||
Keywords | DE NOVO PROTEIN / Allosterically Switchable Protein / sr322 / closed state | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å | ||||||
Authors | Weidle, C. / Borst, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 Title: De Novo Design of Allosterically Switchable Protein Assemblies Authors: Pillai, A. / Idris, A. / Philomin, A. / Weidle, C. / Skotheim, R. / Leung, P. / Broerman, A. / Demakis, C. / Borst, A.J. / Praetorius, F. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8utm.cif.gz | 379.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8utm.ent.gz | 270.2 KB | Display | PDB format |
PDBx/mmJSON format | 8utm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8utm_validation.pdf.gz | 977.6 KB | Display | wwPDB validaton report |
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Full document | 8utm_full_validation.pdf.gz | 977.1 KB | Display | |
Data in XML | 8utm_validation.xml.gz | 63 KB | Display | |
Data in CIF | 8utm_validation.cif.gz | 105.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/8utm ftp://data.pdbj.org/pub/pdb/validation_reports/ut/8utm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 40089.242 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: 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 | Name: sr322 / Type: COMPLEX Details: Complex is made up of 4 monomeric proteins, and is purified as a 4 sided multimer sr322. In this structure two copies of sr322 interact in an off target way. Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 0.326592 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: synthetic construct (others) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) | |||||||||||||||
Buffer solution | pH: 8 / Details: 150 mM NaCl, 40 mM Tris pH 8.0 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.971 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K |
-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 defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5 sec. / Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4213 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 699357 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144551 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT Details: Initial fit was done using Chimera using Rigid body from In silico model. Then Isolde and Namdinator were used. Coot and Phenix were also used. | ||||||||||||||||||||||||
Atomic model building | Type: in silico model | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 176.36 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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