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- PDB-6h6g: Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal... -

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Basic information

Entry
Database: PDB / ID: 6h6g
TitleCrystal Structure of TcdB2-TccC3 without hypervariable C-terminal region
ComponentsTcdB2,TccC3
KeywordsTOXIN / Tc toxin / ABC toxin
Function / homology
Function and homology information


extracellular region / 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 / Rhs repeat-associated core / Integrin alpha, N-terminal
Similarity search - Domain/homology
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsGatsogiannis, C. / Merino, F. / Roderer, D. / Balchin, D. / Schubert, E. / Kuhlee, A. / Hayer-Hartl, M. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Nature / Year: 2018
Title: Tc toxin activation requires unfolding and refolding of a β-propeller.
Authors: Christos Gatsogiannis / Felipe Merino / Daniel Roderer / David Balchin / Evelyn Schubert / Anne Kuhlee / Manajit Hayer-Hartl / Stefan Raunser /
Abstract: Tc toxins secrete toxic enzymes into host cells using a unique syringe-like injection mechanism. They are composed of three subunits, TcA, TcB and TcC. TcA forms the translocation channel and the TcB- ...Tc toxins secrete toxic enzymes into host cells using a unique syringe-like injection mechanism. They are composed of three subunits, TcA, TcB and TcC. TcA forms the translocation channel and the TcB-TcC heterodimer functions as a cocoon that shields the toxic enzyme. Binding of the cocoon to the channel triggers opening of the cocoon and translocation of the toxic enzyme into the channel. Here we show in atomic detail how the assembly of the three components activates the toxin. We find that part of the cocoon completely unfolds and refolds into an alternative conformation upon binding. The presence of the toxic enzyme inside the cocoon is essential for its subnanomolar binding affinity for the TcA subunit. The enzyme passes through a narrow negatively charged constriction site inside the cocoon, probably acting as an extruder that releases the unfolded protein with its C terminus first into the translocation channel.
History
DepositionJul 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TcdB2,TccC3


Theoretical massNumber of molelcules
Total (without water)243,7701
Polymers243,7701
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area86250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.330, 231.330, 141.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TcdB2,TccC3


Mass: 243770.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdB2, TccC3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8GF99, UniProt: Q8GF97
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M tri-sodium citrate pH 5.5, 10 % PEG 8000, 10 % ethylenglycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 87208 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.08 Å / Rmerge(I) obs: 0.5751 / Rpim(I) all: 0.129 / Rrim(I) all: 0.5895

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSBUILT=20160617data reduction
XSCALEBUILT=20160617data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9X

4o9x


Resolution: 3.004→48.639 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 4358 5 %
Rwork0.2157 --
obs0.2175 87159 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.004→48.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17059 0 0 135 17194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317479
X-RAY DIFFRACTIONf_angle_d0.56823830
X-RAY DIFFRACTIONf_dihedral_angle_d13.86510373
X-RAY DIFFRACTIONf_chiral_restr0.0412586
X-RAY DIFFRACTIONf_plane_restr0.0043146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0035-3.03760.41291450.40042757X-RAY DIFFRACTION100
3.0376-3.07340.37311420.36562713X-RAY DIFFRACTION100
3.0734-3.11080.38431440.3582750X-RAY DIFFRACTION100
3.1108-3.15020.36731440.35082729X-RAY DIFFRACTION100
3.1502-3.19160.34461440.32912730X-RAY DIFFRACTION100
3.1916-3.23540.38011440.32522734X-RAY DIFFRACTION100
3.2354-3.28160.34161420.3142694X-RAY DIFFRACTION100
3.2816-3.33050.3171450.30392758X-RAY DIFFRACTION100
3.3305-3.38260.331460.28742763X-RAY DIFFRACTION100
3.3826-3.4380.34161440.2882746X-RAY DIFFRACTION100
3.438-3.49730.31211430.2622717X-RAY DIFFRACTION100
3.4973-3.56090.27311460.24312767X-RAY DIFFRACTION100
3.5609-3.62930.2741440.22792737X-RAY DIFFRACTION100
3.6293-3.70340.25361440.21842741X-RAY DIFFRACTION100
3.7034-3.78390.27311450.22692751X-RAY DIFFRACTION100
3.7839-3.87190.26351450.21442744X-RAY DIFFRACTION100
3.8719-3.96870.2661450.20682770X-RAY DIFFRACTION100
3.9687-4.07590.25641430.18962731X-RAY DIFFRACTION100
4.0759-4.19580.22581460.18152772X-RAY DIFFRACTION100
4.1958-4.33110.18041440.16912732X-RAY DIFFRACTION100
4.3311-4.48580.19971460.16382774X-RAY DIFFRACTION100
4.4858-4.66530.17881450.1462761X-RAY DIFFRACTION100
4.6653-4.87740.18251460.15162770X-RAY DIFFRACTION100
4.8774-5.13430.19851460.16312765X-RAY DIFFRACTION100
5.1343-5.45560.19091470.172788X-RAY DIFFRACTION100
5.4556-5.87620.2411450.19032769X-RAY DIFFRACTION100
5.8762-6.46630.26441480.20642809X-RAY DIFFRACTION100
6.4663-7.39920.22831470.20882785X-RAY DIFFRACTION100
7.3992-9.31140.25581490.19892830X-RAY DIFFRACTION100
9.3114-48.64530.25381540.21982914X-RAY DIFFRACTION100

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