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- PDB-4wj1: Crystal structure of EspB from the ESX-1 type VII secretion system -

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Basic information

Entry
Database: PDB / ID: 4wj1
TitleCrystal structure of EspB from the ESX-1 type VII secretion system
ComponentsAntigen MTB48, Mycobacterial protein
KeywordsPROTEIN TRANSPORT / Mycobacterial protein
Function / homologyESX-1 secretion-associated protein EspB, PE domain / ESX-1 secreted protein B PE domain / identical protein binding / Antigen MTB48
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.415 Å
AuthorsSolomonson, M. / Strynadka, N.C.J.
CitationJournal: Structure / Year: 2015
Title: Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism.
Authors: Matthew Solomonson / Dheva Setiaputra / Karl A T Makepeace / Emilie Lameignere / Evgeniy V Petrotchenko / Deborah G Conrady / Julien R Bergeron / Marija Vuckovic / Frank DiMaio / Christoph H ...Authors: Matthew Solomonson / Dheva Setiaputra / Karl A T Makepeace / Emilie Lameignere / Evgeniy V Petrotchenko / Deborah G Conrady / Julien R Bergeron / Marija Vuckovic / Frank DiMaio / Christoph H Borchers / Calvin K Yip / Natalie C J Strynadka /
Abstract: Mycobacterium tuberculosis (Mtb) uses the ESX-1 type VII secretion system to export virulence proteins across its lipid-rich cell wall, which helps permeabilize the host's macrophage phagosomal ...Mycobacterium tuberculosis (Mtb) uses the ESX-1 type VII secretion system to export virulence proteins across its lipid-rich cell wall, which helps permeabilize the host's macrophage phagosomal membrane, facilitating the escape and cell-to-cell spread of Mtb. ESX-1 membranolytic activity depends on a set of specialized secreted Esp proteins, the structure and specific roles of which are not currently understood. Here, we report the X-ray and electron microscopic structures of the ESX-1-secreted EspB. We demonstrate that EspB adopts a PE/PPE-like fold that mediates oligomerization with apparent heptameric symmetry, generating a barrel-shaped structure with a central pore that we propose contributes to the macrophage killing functions of EspB. Our structural data also reveal unexpected direct interactions between the EspB bipartite secretion signal sequence elements that form a unified aromatic surface. These findings provide insight into how specialized proteins encoded within the ESX-1 locus are targeted for secretion, and for the first time indicate an oligomerization-dependent role for Esp virulence factors.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Antigen MTB48, Mycobacterial protein


Theoretical massNumber of molelcules
Total (without water)31,9361
Polymers31,9361
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Antigen MTB48, Mycobacterial protein

A: Antigen MTB48, Mycobacterial protein


Theoretical massNumber of molelcules
Total (without water)63,8722
Polymers63,8722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2120 Å2
ΔGint-9 kcal/mol
Surface area29060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.749, 125.749, 75.061
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21A-342-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Antigen MTB48, Mycobacterial protein / Uncharacterized protein


Mass: 31935.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0076, MSMEI_0076 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QNK4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 5.36 Å3/Da / Density % sol: 77.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 100 mM HEPES, 540 mM MgCl2, 15% PEG 6000

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.41→62.87 Å / Num. obs: 26601 / % possible obs: 100 % / Redundancy: 21.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.026 / Net I/σ(I): 22.8 / Num. measured all: 580318 / Scaling rejects: 180
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.41-2.5120.70.6115.65774527890.9720.137100
9.04-62.87200.06450.5112565640.9990.01499.4

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Processing

Software
NameVersionClassification
Aimless0.3.5data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementResolution: 2.415→61.803 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.32 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2011 1997 7.53 %
Rwork0.1755 24541 -
obs0.1774 26538 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.02 Å2 / Biso mean: 48.7152 Å2 / Biso min: 22.68 Å2
Refinement stepCycle: final / Resolution: 2.415→61.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 0 152 2329
Biso mean---47.33 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082228
X-RAY DIFFRACTIONf_angle_d1.0333027
X-RAY DIFFRACTIONf_chiral_restr0.038312
X-RAY DIFFRACTIONf_plane_restr0.005413
X-RAY DIFFRACTIONf_dihedral_angle_d15.643818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.415-2.47540.33881410.262317251866100
2.4754-2.54230.29071390.254617331872100
2.5423-2.61710.24891390.23171736187599
2.6171-2.70160.25511390.22421717185699
2.7016-2.79810.27031440.209517501894100
2.7981-2.91020.20881390.211717371876100
2.9102-3.04260.23581420.205517381880100
3.0426-3.2030.19051460.187317401886100
3.203-3.40370.23961390.191417711910100
3.4037-3.66640.18111430.15117201863100
3.6664-4.03540.16181440.147417691913100
4.0354-4.61910.1611430.137417681911100
4.6191-5.81890.17711470.153717881935100
5.8189-61.82280.16831520.153418492001100
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)
12.314-0.6317-2.18160.84520.58413.2942-0.2529-0.1219-0.16030.14720.02210.20260.0223-0.27840.19390.28730.1229-0.02410.4390.00350.301921.574549.410825.1745
21.1186-0.1071-1.5110.93470.6616.3512-0.243-0.4503-0.24030.19510.04460.07010.6331-0.04870.07310.58330.09550.0180.6087-0.03570.348622.405841.789733.2661
31.090.2259-1.32890.0314-0.2372.6011-0.0906-0.1833-0.1170.04020.037-0.0959-0.07960.31680.08710.28210.0852-0.01020.4049-0.01190.341939.463250.18946.8649
41.9668-0.018-1.93610.66050.221.9379-0.3832-0.087-0.3378-0.1095-0.0161-0.24170.03130.27580.23070.2391-0.00340.01540.5773-0.01320.471455.071544.8079-10.058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 101 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 121 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 122 through 227 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 228 through 288 )A0

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