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- PDB-5wez: Structure of the Tir-CesT effector-chaperone complex -

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Basic information

Entry
Database: PDB / ID: 5wez
TitleStructure of the Tir-CesT effector-chaperone complex
Components
  • Tir chaperone
  • Translocated intimin receptor Tir
KeywordsCHAPERONE / effector / complex / secretion / translocation
Function / homology
Function and homology information


protein secretion by the type III secretion system / : / host cell plasma membrane / extracellular region / membrane / cytoplasm
Similarity search - Function
Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family ...Translocated intimin receptor, central domain / Translocated intimin receptor, N-terminal / Translocated intimin receptor / Translocated intimin receptor, C-terminal / Translocated intimin receptor, central domain superfamily / Translocated intimin receptor (Tir) intimin-binding domain / Translocated intimin receptor (Tir) C-terminus / Translocated intimin receptor (Tir) N-terminus / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translocated intimin receptor Tir / Tir chaperone
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsLittle, D.J. / Coombes, B.K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council Discovery Grant341435-2010 RGPIN Canada
CitationJournal: PLoS Pathog. / Year: 2018
Title: Molecular basis for CesT recognition of type III secretion effectors in enteropathogenic Escherichia coli.
Authors: Little, D.J. / Coombes, B.K.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 2023Group: 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: Tir chaperone
B: Translocated intimin receptor Tir


Theoretical massNumber of molelcules
Total (without water)22,2122
Polymers22,2122
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA predicts the dimer interface through the crystallographic two-fold symmetry operator
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-16 kcal/mol
Surface area8760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.960, 66.960, 75.710
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 Tir chaperone


Mass: 15677.607 Da / Num. of mol.: 1 / Fragment: UNP residues 2-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: cesT, E2348C_3940 / Plasmid: pCOLADuet-1 / Details (production host): co-expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus / References: UniProt: P21244
#2: Protein Translocated intimin receptor Tir / Secreted effector protein Tir


Mass: 6534.134 Da / Num. of mol.: 1 / Fragment: UNP residues 32-80
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: tir, espE, E2348C_3941 / Plasmid: pCOLADuet-1 / Details (production host): co-expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus / References: UniProt: B7UM99

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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: 2.21 Å3/Da / Density % sol: 44.24 % / Description: rhombohedrons
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 mM Tris-HCl pH 7.5, 0.2 M MgCl2, 17% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 21, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.74→57.99 Å / Num. obs: 5461 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Net I/σ(I): 13.8
Reflection shellResolution: 2.74→2.88 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 790 / CC1/2: 0.56 / Rpim(I) all: 0.33 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLM7.1.1data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K3E

1k3e


Resolution: 2.74→57.989 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 279 5.11 %Random
Rwork0.2085 ---
obs0.2112 5457 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.74→57.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 0 0 1170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011193
X-RAY DIFFRACTIONf_angle_d1.3431625
X-RAY DIFFRACTIONf_dihedral_angle_d15.811710
X-RAY DIFFRACTIONf_chiral_restr0.058189
X-RAY DIFFRACTIONf_plane_restr0.008211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.735-3.44580.31851270.31042557X-RAY DIFFRACTION100
3.4458-58.00210.24421520.18872621X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20271.17242.23058.9308-1.18325.58621.48021.60172.2527-0.8283-1.1317-1.0002-1.3566-1.7765-0.2391.35910.55080.22511.25530.33071.17112.844336.735717.6135
28.10433.47841.93228.3586-5.75177.25020.60241.63810.4662-1.9841-1.03770.68680.8058-1.23920.46691.13480.3160.02171.0171-0.11091.04248.414226.170220.3893
32.4044-3.59943.46575.3824-5.18524.98981.8072-1.14641.2363-0.46982.70176.34532.28382.5118-2.8152.166-0.2446-0.43911.4222-0.24391.94444.77854.48329.0293
41.8463-3.96522.31098.363-4.72669.53190.31370.10460.0397-0.9072-1.0160.35041.5577-0.33860.58560.83680.08410.23430.6781-0.17760.946711.346118.560133.1815
55.9379-2.77821.38431.3163-1.06116.30360.68070.8479-0.4417-3.216-2.4475-1.25611.60430.47921.43121.08770.36340.36720.8563-0.01911.474919.253818.78926.2017
66.48012.25976.58983.43245.12459.70971.0864.18763.1403-2.2735-2.29920.4889-0.40350.6882-0.06071.44230.52310.31431.8470.06281.345822.433826.523312.133
77.30776.3702-8.19515.5604-7.07469.82160.99292.9801-0.9788-2.99990.82431.42043.5134-0.1774-1.92192.1010.9766-0.40981.94770.02590.86622.217221.492114.2823
86.0945-1.97592.1492.4377-2.79487.30821.06490.12960.46280.3833-0.99361.24732.31060.6785-0.38511.75740.0153-0.25851.28750.07541.51889.688621.854811.5081
94.8918-3.9197-3.8754.5733.77656.6907-3.9986-2.79310.87442.04622.67411.541.5113-0.46990.68251.66150.0094-0.40672.3513-0.56321.44250.12219.064423.8533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 43 )
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 53 )
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 75 )

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