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Yorodumi- PDB-8rtd: Stalk-Arches-IMC structure from the fully-assembled R388 type IV ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rtd | |||||||||||||||
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Title | Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM. | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / type IV secretion system type 4 secretion system T4SS Arches Stalk inner membrane complex IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB5 VirB6 VirB8 VirB10 TrwM TrwK TrwJ TrwI TrwG TrwE | |||||||||||||||
Function / homology | Function and homology information protein secretion by the type IV secretion system / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.33 Å | |||||||||||||||
Authors | Mace, K. / Waksman, G. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: To Be Published / Year: 2024 Title: Cryo-EM structure of a conjugative type 4 secretion system identifies a molecular switch regulating conjugative pilus biogenesis Authors: Mace, K. / Waksman, G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rtd.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rtd.ent.gz | 791.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rtd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8rtd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8rtd_validation.xml.gz | 171.4 KB | Display | |
Data in CIF | 8rtd_validation.cif.gz | 286.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/8rtd ftp://data.pdbj.org/pub/pdb/validation_reports/rt/8rtd | HTTPS FTP |
-Related structure data
Related structure data | 19488MC 8rt4C 8rt5C 8rt6C 8rt7C 8rt8C 8rt9C 8rtaC 8rtbC 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
-Protein , 6 types, 34 molecules ABCKEDFGQSUXYbcdiaZeLMHIJjRfOP...
#1: Protein | Mass: 25190.461 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwJ / Production host: Escherichia coli (E. coli) / References: UniProt: A8R752 #2: Protein | Mass: 25799.994 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwG / Production host: Escherichia coli (E. coli) / References: UniProt: A8R756 #3: Protein | Mass: 42443.785 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwE / Production host: Escherichia coli (E. coli) / References: UniProt: A8R758 #4: Protein | Mass: 35324.172 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwI / Production host: Escherichia coli (E. coli) / References: UniProt: A8R754 #5: Protein | Mass: 12292.585 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwM / Production host: Escherichia coli (E. coli) / References: UniProt: A8R750 #6: Protein | Mass: 93769.930 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Sequence from conjugative plasmid R388 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trwK / Production host: Escherichia coli (E. coli) / References: UniProt: A8R751 |
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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: Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 3300 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 57.5 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: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65173 / Symmetry type: POINT |