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Yorodumi- PDB-8cq2: Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cq2 | ||||||
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Title | Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C mutant | ||||||
Components | TcdA1 | ||||||
Keywords | TOXIN / Bacterial toxin / Tc toxin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Photorhabdus luminescens (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Nganga, P.N. / Roderer, D. / Belyy, A. / Prumbaum, D. / Raunser, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: to be published Title: Kinetics of the syringe-like injection mechanism of Tc toxins Authors: Nganga, P.N. / Folz, J. / Kucher, S. / Roderer, D. / Xu, Y. / Sitsel, O. / Belyy, A. / Prumbaum, D. / Assafa, T.E. / Kuehnemuth, R. / Dong, M. / Seidel, C. / Bordignon, E. / Raunser, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cq2.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8cq2.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8cq2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cq2_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cq2_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8cq2_validation.xml.gz | 249.9 KB | Display | |
Data in CIF | 8cq2_validation.cif.gz | 389.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cq2 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cq2 | HTTPS FTP |
-Related structure data
Related structure data | 16793MC 8cpzC 8cq0C 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: 285329.625 Da / Num. of mol.: 5 / Mutation: C16S C20S C870S T1279C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdA, tcdA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: Q9RN43 |
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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: TcdA1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 1.5 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Photorhabdus luminescens (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 RIPL / Plasmid: pET19 | ||||||||||||||||||||
Buffer solution | pH: 11.2 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid type: Quantifoil | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 286 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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 78 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13059 |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 573814 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80710 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Refine LS restraints |
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