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Yorodumi- PDB-8w22: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w22 | ||||||
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Title | Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1) | ||||||
Components |
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Keywords | TOXIN / Streptomyces / Umbrella toxin particles / Alanine leucine phenylalanine-rich (ALF) repeat proteins / Seattle structural genomics center for infectious disease / SSGCID | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Park, Y.J. / Zhao, Q. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio, F. / Mougous, J.D. / Veesler, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2024 Title: Streptomyces umbrella toxin particles block hyphal growth of competing species Authors: Park, Y.J. / Veesler, D. / Mougous, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w22.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w22.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 8w22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/8w22 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/8w22 | HTTPS FTP |
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-Related structure data
Related structure data | 43737MC 8w20C 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: 142716.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: endogenous tags to purified the complex from natural source Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV2 |
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#2: Protein | Mass: 17186.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV3 |
#3: Protein | Mass: 54437.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: endogenous tags to purified the complex from natural source Source: (natural) Streptomyces coelicolor A3(2) (bacteria) / References: UniProt: Q9ACV4 |
-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: Umb1 umbrella toxin particle (local refinement of UmbB1 bound ALF of UmbC1 and UmbA1) Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Streptomyces coelicolor A3(2) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 200 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386275 / Symmetry type: POINT |