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- PDB-8ako: Structure of EspB-EspK complex: the non-identical twin of the PE-... -

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Basic information

Entry
Database: PDB / ID: 8ako
TitleStructure of EspB-EspK complex: the non-identical twin of the PE-PPE-EspG secretion mechanism.
Components
  • ESX-1 secretion-associated protein EspB
  • ESX-1 secretion-associated protein EspK
KeywordsCHAPERONE / Secretion Mycrobial protein Virulence factor
Function / homology
Function and homology information


protein secretion by the type VII secretion system / symbiont-mediated suppression of host autophagy / biological process involved in interaction with host / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
ESX-1 secretion-associated protein EspB, PE domain / : / ESX-1 secreted protein B PE domain / ESX-1 secretion-associated protein EspB, PPE domain / ESAT-6-like superfamily / PPE superfamily
Similarity search - Domain/homology
ESX-1 secretion-associated protein EspK / ESX-1 secretion-associated protein EspB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.293 Å
AuthorsGijsbers, A. / Eymery, M. / Menart, I. / Vinciauskaite, V. / Gao, Y. / Siliqi, D. / Peters, P. / Mccarthy, A. / Ravelli, R.B.G.
Funding support Netherlands, European Union, France, 4items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)731.016.407 Netherlands
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
European Union (EU)766970European Union
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05-02 France
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The crystal structure of the EspB-EspK virulence factor-chaperone complex suggests an additional type VII secretion mechanism in Mycobacterium tuberculosis.
Authors: Gijsbers, A. / Eymery, M. / Gao, Y. / Menart, I. / Vinciauskaite, V. / Siliqi, D. / Peters, P.J. / McCarthy, A. / Ravelli, R.B.G.
History
DepositionJul 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESX-1 secretion-associated protein EspB
B: ESX-1 secretion-associated protein EspK


Theoretical massNumber of molelcules
Total (without water)59,1592
Polymers59,1592
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.579, 101.579, 377.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ESX-1 secretion-associated protein EspB / Antigen MTB48


Mass: 32711.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: espB, mtb48, Rv3881c, MTV027.16c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJD9
#2: Protein ESX-1 secretion-associated protein EspK


Mass: 26447.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: espK, Rv3879c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJC1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 5.06 Å3/Da / Density % sol: 75.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2-1.2 M sodium malonate 0.1 M HEPES (pH 7.8) 8-14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 12, 2021
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.29→85.82 Å / Num. obs: 28129 / % possible obs: 53.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 63.86 Å2 / Rpim(I) all: 0.034 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.6 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1406 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XXX

4xxx


Resolution: 2.293→85.816 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.247 / Average fsc free: 0.8555 / Average fsc work: 0.8707 / Cross valid method: THROUGHOUT / ESU R Free: 0.308
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 1444 5.133 %RANDOM
Rwork0.2348 26685 --
all0.237 ---
obs-28129 53.194 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 84.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.034 Å2-0.017 Å2-0 Å2
2---0.034 Å20 Å2
3---0.111 Å2
Refinement stepCycle: LAST / Resolution: 2.293→85.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3892 0 0 38 3930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123980
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.6395436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90322.5216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01115612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1251529
X-RAY DIFFRACTIONr_chiral_restr0.0950.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023107
X-RAY DIFFRACTIONr_nbd_refined0.170.21694
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22733
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.278
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.219
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.21
X-RAY DIFFRACTIONr_mcbond_it08.3792023
X-RAY DIFFRACTIONr_mcangle_it012.5672526
X-RAY DIFFRACTIONr_scbond_it08.4161955
X-RAY DIFFRACTIONr_scangle_it012.492910
X-RAY DIFFRACTIONr_lrange_it0111.0435769
X-RAY DIFFRACTIONr_rigid_bond_restr8.39433978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.293-2.3520.43230.529108X-RAY DIFFRACTION2.8936
2.352-2.4170.686110.45297X-RAY DIFFRACTION8.2796
2.417-2.4870.369200.383367X-RAY DIFFRACTION10.6553
2.487-2.5630.419140.386453X-RAY DIFFRACTION13.32
2.563-2.6470.402280.332586X-RAY DIFFRACTION17.9795
2.647-2.740.376480.32694X-RAY DIFFRACTION22.1757
2.74-2.8430.356530.342855X-RAY DIFFRACTION28.2778
2.843-2.9590.386630.321158X-RAY DIFFRACTION39.7073
2.959-3.0910.386770.3151543X-RAY DIFFRACTION54
3.091-3.2410.3611130.3122389X-RAY DIFFRACTION88.3163
3.241-3.4170.3251690.2972560X-RAY DIFFRACTION99.6713
3.417-3.6230.2981220.2492476X-RAY DIFFRACTION99.9231
3.623-3.8730.2691390.2312276X-RAY DIFFRACTION99.711
3.873-4.1830.2551190.2262172X-RAY DIFFRACTION99.7822
4.183-4.5810.2841110.2062010X-RAY DIFFRACTION99.8118
4.581-5.120.278830.2051849X-RAY DIFFRACTION99.7419
5.12-5.9090.27940.231639X-RAY DIFFRACTION99.5977
5.909-7.2290.231780.2231418X-RAY DIFFRACTION99.8665
7.229-10.1880.194620.1641137X-RAY DIFFRACTION99.6675
10.188-85.8160.292370.226698X-RAY DIFFRACTION98.3936

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