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- PDB-6vhr: Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) sec... -

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Basic information

Entry
Database: PDB / ID: 6vhr
TitleStructure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group I422
Components
  • ESX-3 secretion-associated protein EspG3
  • PE family immunomodulator PE5
  • PPE family protein PPE4
KeywordsPROTEIN TRANSPORT / chaperone / protein secretion
Function / homology
Function and homology information


response to host immune response / cell envelope / cell surface / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
PPE-PPW subfamily, C-terminal / PPE-PPW subfamily C-terminal region / PPE family / PPE family / PE-PGRS family, N-terminal / PE family / EspG family / EspG family / PPE superfamily
Similarity search - Domain/homology
Conserved protein / PE family immunomodulator PE5 / PPE family protein PPE4
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWilliamson, Z.A. / Korotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI119022 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: PE5-PPE4-EspG3heterotrimer structure from mycobacterial ESX-3 secretion system gives insight into cognate substrate recognition by ESX systems.
Authors: Williamson, Z.A. / Chaton, C.T. / Ciocca, W.A. / Korotkova, N. / Korotkov, K.V.
History
DepositionJan 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 11, 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: PE family immunomodulator PE5
B: PPE family protein PPE4
C: ESX-3 secretion-associated protein EspG3


Theoretical massNumber of molelcules
Total (without water)58,2043
Polymers58,2043
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-63 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.090, 219.090, 104.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein PE family immunomodulator PE5


Mass: 9228.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PE5, Rv0285, LH57_01560 / Plasmid: pRSF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: L7N695
#2: Protein PPE family protein PPE4


Mass: 18099.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment residues 1-178
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: PPE4, Rv0286 / Plasmid: pRSF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: P9WI43
#3: Protein ESX-3 secretion-associated protein EspG3


Mass: 30875.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fragment residues 5-290
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: MMAR_0548 / Plasmid: pCDF-21d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: B2HNX0

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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: 5.38 Å3/Da / Density % sol: 77.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2M sodium chloride, 0.1M BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 5, 2018
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→35.727 Å / Num. obs: 19380 / % possible obs: 99.8 % / Redundancy: 10.295 % / Biso Wilson estimate: 125.541 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.091 / Χ2: 1.046 / Net I/σ(I): 15.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.399.5332.1821.3113404140614060.5972.308100
3.39-3.4810.961.7921.815289139613950.7791.87999.9
3.48-3.5810.9761.1522.7614445131713160.8871.20899.9
3.58-3.6910.9610.8343.5814238129912990.940.875100
3.69-3.8110.8450.5495.0113751126912680.9730.57699.9
3.81-3.9410.7580.4156.3913125122012200.980.436100
3.94-4.0910.6470.2798.5912691119211920.9910.293100
4.09-4.2610.5410.20111.4811837112511230.9940.21299.8
4.26-4.4510.3150.15314.0911419110711070.9960.161100
4.45-4.6710.0160.12117.8310607105910590.9960.128100
4.67-4.928.9550.09919.6588219899850.9960.10699.6
4.92-5.2210.3480.09821.3298729549540.9970.103100
5.22-5.5810.8480.08724.5195908848840.9980.091100
5.58-6.0210.6880.08127.1590538478470.9980.085100
6.02-6.610.3960.06330.9180577757750.9990.066100
6.6-7.3810.1120.04936.8772207147140.9990.052100
7.38-8.529.3950.04144.1558816266260.9990.044100
8.52-10.448.2820.03446.2944895475420.9990.03699.1
10.44-14.769.1720.03450.3739354304290.9990.03799.8
14.76-35.7277.4980.03745.3317922652390.9990.0490.2

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018 BUILT=20180319data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180319data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2g38, 4l4w

2g38

4l4w


Resolution: 3.3→35.727 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 1739 4.77 %
Rwork0.2476 --
obs0.2485 19335 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 330.77 Å2 / Biso mean: 190.6195 Å2 / Biso min: 80.02 Å2
Refinement stepCycle: final / Resolution: 3.3→35.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 0 0 3643
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023729
X-RAY DIFFRACTIONf_angle_d0.5035121
X-RAY DIFFRACTIONf_dihedral_angle_d7.7352176
X-RAY DIFFRACTIONf_chiral_restr0.037604
X-RAY DIFFRACTIONf_plane_restr0.004666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.3970.42731320.4028290999
3.397-3.50650.41491200.3546288799
3.5065-3.63170.36391370.32932904100
3.6317-3.7770.31461610.31832848100
3.777-3.94870.32131490.30682880100
3.9487-4.15660.28531290.2871291799
4.1566-4.41660.25871620.26232888100
4.4166-4.75680.27981560.24562869100
4.7568-5.23420.28221410.26222917100
5.2342-5.98850.26341290.28562889100
5.9885-7.53330.31221450.25032899100
7.5333-35.7270.21411780.1822875100

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