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- PDB-4o9x: Crystal Structure of TcdB2-TccC3 -

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Basic information

Entry
Database: PDB / ID: 4o9x
TitleCrystal Structure of TcdB2-TccC3
ComponentsTcdB2, TccC3
KeywordsTOXIN / beta sheet / cocoon / unfolding / tc toxin
Function / homology
Function and homology information


extracellular region / cytoplasm
Similarity search - Function
Shell / RHS repeat-associated core / RHS repeat-associated core / 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 ...Shell / RHS repeat-associated core / RHS repeat-associated core / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsMeusch, D. / Gatsogiannis, C. / Efremov, R.G. / Lang, A.E. / Hofnagel, O. / Vetter, I.R. / Aktories, K. / Raunser, S.
CitationJournal: Nature / Year: 2014
Title: Mechanism of Tc toxin action revealed in molecular detail.
Authors: Dominic Meusch / Christos Gatsogiannis / Rouslan G Efremov / Alexander E Lang / Oliver Hofnagel / Ingrid R Vetter / Klaus Aktories / Stefan Raunser /
Abstract: Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell, including in humans. The underlying mechanism is complex but poorly ...Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell, including in humans. The underlying mechanism is complex but poorly understood. Here we report the first, to our knowledge, high-resolution structures of a TcA subunit in its prepore and pore state and of a complete 1.7 megadalton Tc complex. The structures reveal that, in addition to a translocation channel, TcA forms four receptor-binding sites and a neuraminidase-like region, which are important for its host specificity. pH-induced opening of the shell releases an entropic spring that drives the injection of the TcA channel into the membrane. Binding of TcB/TcC to TcA opens a gate formed by a six-bladed β-propeller and results in a continuous protein translocation channel, whose architecture and properties suggest a novel mode of protein unfolding and translocation. Our results allow us to understand key steps of infections involving Tc toxins at the molecular level.
History
DepositionJan 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TcdB2, TccC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,12910
Polymers247,3231
Non-polymers1,8059
Water17,709983
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)232.360, 232.360, 143.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TcdB2, TccC3


Mass: 247323.250 Da / Num. of mol.: 1 / Fragment: UNP Q8GF97 RESIDUES 1-678
Source method: isolated from a genetically manipulated source
Details: TcdB2, TccC3 chimera / Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdB2, TccC3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8GF99, UniProt: Q8GF97
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 983 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.52 Å3/Da / Density % sol: 72.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Trisodium citrate pH 5.5, 0.1 M MgCl2, 0.1 M NaCl and 12 % PEG 4,000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA11.00717
SYNCHROTRONSLS X10SA21.07169
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.007171
21.071691
ReflectionResolution: 2.17→30 Å / Num. obs: 183387 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.937 Å2 / Rmerge(I) obs: 0.178 / Net I/σ(I): 17.47

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→29.773 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8489 / SU ML: 0.25 / σ(F): 1.99 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 10883 5 %RANDOM
Rwork0.1922 ---
obs0.1934 183387 92.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 348.45 Å2 / Biso mean: 41.1492 Å2 / Biso min: 16.77 Å2
Refinement stepCycle: LAST / Resolution: 2.17→29.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16589 0 9 983 17581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817001
X-RAY DIFFRACTIONf_angle_d1.16623181
X-RAY DIFFRACTIONf_chiral_restr0.0782514
X-RAY DIFFRACTIONf_plane_restr0.0053061
X-RAY DIFFRACTIONf_dihedral_angle_d14.3646219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.19520.39422950.35825566586139
2.1952-2.2210.33744820.33259121960363
2.221-2.2480.34735180.313698561037468
2.248-2.27650.32865570.2987105541111172
2.2765-2.30640.3225840.2838110561164077
2.3064-2.3380.31256280.2756118331246181
2.338-2.37140.29686560.2664124341309086
2.3714-2.40680.27297190.2556135401425994
2.4068-2.44440.26817560.2602143921514899
2.4444-2.48440.26487640.24541450615270100
2.4844-2.52730.28757590.22811444615205100
2.5273-2.57320.25537600.2251451915279100
2.5732-2.62260.25297600.22151448615246100
2.6226-2.67610.25267690.21941456815337100
2.6761-2.73430.24777610.21151449815259100
2.7343-2.79790.23627600.20971445515215100
2.7979-2.86780.23287680.20761456215330100
2.8678-2.94520.22747620.20451446915231100
2.9452-3.03180.22787690.19651450315272100
3.0318-3.12960.22137570.19541451715274100
3.1296-3.24130.22737690.19381447415243100
3.2413-3.37090.20277620.18781455915321100
3.3709-3.52410.20217610.17561447815239100
3.5241-3.70960.17247660.16581454515311100
3.7096-3.94150.1787650.15551449815263100
3.9415-4.2450.17617620.14971450715269100
4.245-4.67080.14327590.13171450015259100
4.6708-5.34330.17367680.14331456415332100
5.3433-6.71920.19457570.17361446015217100
6.7192-29.7760.19657650.1871451215277100
Refinement TLS params.Method: refined / Origin x: 110.3245 Å / Origin y: -31.9852 Å / Origin z: -61.6071 Å
111213212223313233
T0.2393 Å2-0.0134 Å20.0016 Å2-0.1375 Å2-0.0114 Å2--0.205 Å2
L0.1887 °20.0634 °2-0.0339 °2-0.1566 °2-0.0346 °2--0.2912 °2
S0.0106 Å °-0.0112 Å °0.0618 Å °-0.0321 Å °0.0043 Å °0.0218 Å °-0.0685 Å °-0.0148 Å °-0.0117 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA41 - 1295
2X-RAY DIFFRACTION1allA1351 - 1503
3X-RAY DIFFRACTION1allA1518 - 2191
4X-RAY DIFFRACTION1allA1 - 2208
5X-RAY DIFFRACTION1allA9 - 2209
6X-RAY DIFFRACTION1allA1 - 3283

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