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

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Basic information

Entry
Database: PDB / ID: 6uuj
TitleStructure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group P212121
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 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
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PE family immunomodulator PE5
B: PPE family protein PPE4
C: ESX-3 secretion-associated protein EspG3
D: PE family immunomodulator PE5
E: PPE family protein PPE4
F: ESX-3 secretion-associated protein EspG3
G: PE family immunomodulator PE5
H: PPE family protein PPE4
I: ESX-3 secretion-associated protein EspG3
J: PE family immunomodulator PE5
K: PPE family protein PPE4
L: ESX-3 secretion-associated protein EspG3


Theoretical massNumber of molelcules
Total (without water)232,81412
Polymers232,81412
Non-polymers00
Water724
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: PE family immunomodulator PE5
E: PPE family protein PPE4
F: ESX-3 secretion-associated protein EspG3


Theoretical massNumber of molelcules
Total (without water)58,2043
Polymers58,2043
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: PE family immunomodulator PE5
H: PPE family protein PPE4
I: ESX-3 secretion-associated protein EspG3


Theoretical massNumber of molelcules
Total (without water)58,2043
Polymers58,2043
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: PE family immunomodulator PE5
K: PPE family protein PPE4
L: ESX-3 secretion-associated protein EspG3


Theoretical massNumber of molelcules
Total (without water)58,2043
Polymers58,2043
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.265, 158.630, 209.314
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 7 through 77)
21chain D
31(chain G and resid 7 through 77)
41chain J
12(chain B and (resid 2 through 60 or resid 65 through 167))
22(chain E and (resid 2 through 60 or resid 65 through 167))
32chain H
42(chain K and resid 2 through 167)
13chain C
23chain F
33chain I
43chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROVALVAL(chain A and resid 7 through 77)AA7 - 775 - 75
211PROPROVALVALchain DDD7 - 775 - 75
311PROPROVALVAL(chain G and resid 7 through 77)GG7 - 775 - 75
411PROPROVALVALchain JJJ7 - 775 - 75
112ALAALATRPTRP(chain B and (resid 2 through 60 or resid 65 through 167))BB2 - 602 - 60
122ALAALASERSER(chain B and (resid 2 through 60 or resid 65 through 167))BB65 - 16765 - 167
212ALAALATRPTRP(chain E and (resid 2 through 60 or resid 65 through 167))EE2 - 602 - 60
222ALAALASERSER(chain E and (resid 2 through 60 or resid 65 through 167))EE65 - 16765 - 167
312ALAALASERSERchain HHH2 - 1672 - 167
412ALAALASERSER(chain K and resid 2 through 167)KK2 - 1672 - 167
113ASNASNPHEPHEchain CCC6 - 2844 - 282
213ASNASNPHEPHEchain FFF6 - 2844 - 282
313ASNASNPHEPHEchain III6 - 2844 - 282
413ASNASNPHEPHEchain LLL6 - 2844 - 282

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PE family immunomodulator PE5


Mass: 9228.199 Da / Num. of mol.: 4
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.: 4
Source method: isolated from a genetically manipulated source
Details: 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.: 4
Source method: isolated from a genetically manipulated source
Details: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium tartrate dibasic, 20% PEG3350 / PH range: 6.3-6.9

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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→39.515 Å / Num. obs: 48621 / % possible obs: 99.1 % / Redundancy: 4.222 % / Biso Wilson estimate: 80.805 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.131 / Rrim(I) all: 0.149 / Χ2: 1.006 / Net I/σ(I): 9.45 / Num. measured all: 205287 / Scaling rejects: 30
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
3-3.084.3511.5631.1415336354335250.591.77999.5
3.08-3.164.261.3381.3214871351434910.6961.52899.3
3.16-3.254.1491.1111.5313892339333480.7361.27498.7
3.25-3.353.8260.7861.9512267328232060.7940.91197.7
3.35-3.464.370.6742.6514010321632060.8630.76599.7
3.46-3.594.4720.5193.313828310230920.9040.58799.7
3.59-3.724.4610.3454.7613222297329640.9510.3999.7
3.72-3.874.4150.2895.6412745289828870.9670.32799.6
3.87-4.054.3460.2147.0112104279227850.9850.24399.7
4.05-4.244.2640.1569.0111295265826490.990.17899.7
4.24-4.474.1770.1111.9910550253125260.9940.12699.8
4.47-4.743.980.08214.29412237823650.9960.09499.5
4.74-5.073.8610.07414.538490228221990.9970.08596.4
5.07-5.484.4020.07615.749284212321090.9980.08699.3
5.48-64.3650.07815.838530195919540.9970.08999.7
6-6.714.3230.06918.367699178417810.9960.07899.8
6.71-7.754.1090.04325.316423157115630.9980.0599.5
7.75-9.493.7180.02635.484934135913270.9990.0397.6
9.49-13.424.0130.0242.584206108510480.9990.02496.6
13.42-39.5153.6730.01938.48218964259610.02292.8

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Processing

Software
NameVersionClassification
XSCALEVERSION Mar 15, 2019 BUILT=20190606data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSVERSION Jan 26, 2018 BUILT=20180319data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VHR

6vhr


Resolution: 3→39.515 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.86
RfactorNum. reflection% reflection
Rfree0.3015 2462 5.08 %
Rwork0.266 --
obs0.2679 48463 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 286.52 Å2 / Biso mean: 101.6 Å2 / Biso min: 28.25 Å2
Refinement stepCycle: final / Resolution: 3→39.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14535 0 0 4 14539
Biso mean---70.63 -
Num. residues----1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214875
X-RAY DIFFRACTIONf_angle_d0.52820416
X-RAY DIFFRACTIONf_dihedral_angle_d7.2948684
X-RAY DIFFRACTIONf_chiral_restr0.0382406
X-RAY DIFFRACTIONf_plane_restr0.0032651
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1175X-RAY DIFFRACTION6.57TORSIONAL
12D1175X-RAY DIFFRACTION6.57TORSIONAL
13G1175X-RAY DIFFRACTION6.57TORSIONAL
14J1175X-RAY DIFFRACTION6.57TORSIONAL
21B2743X-RAY DIFFRACTION6.57TORSIONAL
22E2743X-RAY DIFFRACTION6.57TORSIONAL
23H2743X-RAY DIFFRACTION6.57TORSIONAL
24K2743X-RAY DIFFRACTION6.57TORSIONAL
31C4873X-RAY DIFFRACTION6.57TORSIONAL
32F4873X-RAY DIFFRACTION6.57TORSIONAL
33I4873X-RAY DIFFRACTION6.57TORSIONAL
34L4873X-RAY DIFFRACTION6.57TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.05770.41141370.4176250399
3.0577-3.12010.44421260.3951253899
3.1201-3.18790.41941330.3792249999
3.1879-3.2620.41591280.3635247597
3.262-3.34360.42511260.3447248997
3.3436-3.43390.37731210.3236257399
3.4339-3.53490.35481170.33052542100
3.5349-3.64890.37561400.2973255799
3.6489-3.77920.3571280.27362568100
3.7792-3.93040.34241300.2718253199
3.9304-4.10910.30841430.2621257399
4.1091-4.32550.2711340.25172573100
4.3255-4.59620.28091520.22962556100
4.5962-4.95040.29621390.2258251197
4.9504-5.44740.26291400.2371259699
5.4474-6.2330.32951490.27812591100
6.233-7.84290.29741720.25682621100
7.8429-39.5150.20491470.2157270597

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