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- PDB-6l7i: Signal substraction of TcdB1-TccC2 and part of TcdA1 -

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Basic information

Entry
Database: PDB / ID: 6l7i
TitleSignal substraction of TcdB1-TccC2 and part of TcdA1
Components
  • (TccC2) x 2
  • TcdA1
  • TcdB1
KeywordsTOXIN/PROTEIN TRANSPORT / protein transportation / TcdA1 / TcdB1 / TccC2 / TOXIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / : / TcdA1, receptor binding domain ...Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / : / TcdA1, receptor binding domain / : / TcdA1, receptor binding domain / ABC toxin, N-terminal domain / ABC toxin N-terminal region / TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / Rhs repeat-associated core / : / Integrin alpha, N-terminal
Similarity search - Domain/homology
TccC2 / TcdB1 / TcdA1
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYan, Z.F. / Yang, G.W.
CitationJournal: To Be Published
Title: Signal substraction of TcdB1-TccC2 and part of TcdA1
Authors: Yan, Z.F. / Zhang, N. / Yang, G.W.
History
DepositionNov 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: TcdA1
B: TcdA1
C: TcdA1
D: TcdA1
E: TcdA1
F: TcdB1
G: TccC2
H: TccC2


Theoretical massNumber of molelcules
Total (without water)343,2408
Polymers343,2408
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26800 Å2
ΔGint-114 kcal/mol
Surface area116810 Å2

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Components

#1: Protein
TcdA1 / Toxin A


Mass: 20255.887 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdA, tcdA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RN43
#2: Protein TcdB1


Mass: 165296.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93EP6
#3: Protein TccC2


Mass: 74759.125 Da / Num. of mol.: 1 / Fragment: N terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: TccC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93EP1
#4: Protein/peptide TccC2


Mass: 1905.087 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: TccC2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93EP1
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Toxin complex TcdA1-TcdB1-TccC2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124828 / Symmetry type: POINT

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