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- PDB-4g1i: Structure of the PrgH periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 4g1i
TitleStructure of the PrgH periplasmic domain
ComponentsProtein prgH
KeywordsCELL INVASION / Ring-building motif / Type III secretion / InvG
Function / homology
Function and homology information


GMP Synthetase; Chain A, domain 3 - #170 / Alpha-Beta Plaits - #1780 / Alpha-Beta Plaits - #1770 / Type III secretion system, PrgH/EprH / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / GMP Synthetase; Chain A, domain 3 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein PrgH
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBergeron, J.R.C. / Worrall, L.J. / Strynadka, N.C.J.
CitationJournal: PLoS Pathog / Year: 2013
Title: A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly.
Authors: Julien R C Bergeron / Liam J Worrall / Nikolaos G Sgourakis / Frank DiMaio / Richard A Pfuetzner / Heather B Felise / Marija Vuckovic / Angel C Yu / Samuel I Miller / David Baker / Natalie C J Strynadka /
Abstract: The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed ...The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein prgH
B: Protein prgH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,27910
Polymers52,9462
Non-polymers1,3338
Water4,197233
1
A: Protein prgH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1395
Polymers26,4731
Non-polymers6664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein prgH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1395
Polymers26,4731
Non-polymers6664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)264.432, 33.380, 48.530
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsThough the cloned protein construct that was crystallized is a monomer, the full-length version of this protein forms a 24-mer.

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Components

#1: Protein Protein prgH


Mass: 26472.988 Da / Num. of mol.: 2 / Fragment: UNP residues 170-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: prgH, STM2874 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41783
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Bicine, pH 8.5, 20% PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 1, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 43189 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GR0

3gr0


Resolution: 1.85→45.957 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2139 1835 5.01 %
Rwork0.1736 --
obs0.1758 36630 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7682 Å2-0 Å2-5.6761 Å2
2---7.96 Å2-0 Å2
3---6.1918 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 76 233 3491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153320
X-RAY DIFFRACTIONf_angle_d1.5454464
X-RAY DIFFRACTIONf_dihedral_angle_d18.0061281
X-RAY DIFFRACTIONf_chiral_restr0.118463
X-RAY DIFFRACTIONf_plane_restr0.007572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31631300.23852656X-RAY DIFFRACTION100
1.9-1.95590.26531440.20812688X-RAY DIFFRACTION100
1.9559-2.01910.25491400.19712640X-RAY DIFFRACTION100
2.0191-2.09120.24621400.18362670X-RAY DIFFRACTION100
2.0912-2.1750.1971390.17992649X-RAY DIFFRACTION100
2.175-2.27390.23861400.16942658X-RAY DIFFRACTION100
2.2739-2.39380.23571350.1752683X-RAY DIFFRACTION100
2.3938-2.54380.19671330.16142691X-RAY DIFFRACTION100
2.5438-2.74020.21861470.17242667X-RAY DIFFRACTION100
2.7402-3.01590.20551440.16592688X-RAY DIFFRACTION99
3.0159-3.45220.20661320.16692688X-RAY DIFFRACTION99
3.4522-4.34880.19521610.15142682X-RAY DIFFRACTION99
4.3488-45.97140.21241500.18982735X-RAY DIFFRACTION96
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)
10.01460.01880.0511-0.00080.010.0083-0.3658-0.21530.43760.5110.44480.3517-0.00420.347100.57110.143-0.02720.4950.0470.3177-43.6965-0.690231.7675
20.0446-0.0890.04770.10580.00380.06650.1137-0.2301-0.10690.19970.101-0.30910.5127-0.004600.5185-0.043-0.05750.31890.07270.266-49.9071-1.327223.1334
3-0.01060.05820.00140.0024-0.00760.0495-0.1061-0.1380.19180.13690.0958-0.28180.17430.3169-00.58040.1192-0.18640.3485-0.05230.3654-36.8297-3.65623.2645
4-0.01850.03530.0039-0.0138-0.0338-0.0149-0.23980.0656-0.1549-0.2839-0.22830.488-0.03620.3313-00.60380.0114-0.01320.25620.04580.3545-45.5288-11.343225.123
50.53520.7077-0.14850.92210.0646-0.25380.0438-0.0032-0.03670.0616-0.07530.04630.04830.0447-00.1545-0.0036-0.00760.10120.01870.1148-54.4527.24848.7686
6-0.0110.00230.01210.0224-0.0606-0.00040.0384-0.0791-0.12910.2594-0.03580.3742-0.105-0.089-00.2008-0.01220.02980.2286-0.01350.263-67.88876.5547.9584
70.3584-0.3818-0.03440.41820.28460.02250.0074-0.06490.15830.07790.04080.15350.0093-0.045700.1551-0.0119-0.01130.15350.01730.1375-54.683714.289710.2586
80.137-0.0485-0.17870.1192-0.09880.37180.20370.07850.3154-0.2543-0.2516-0.20380.0931-0.0441-00.25780.02040.08920.28480.06310.2701-41.227123.5738-4.6858
90.13520.1147-0.23340.4043-0.00350.2211-0.0198-0.0741-0.0618-0.04740.06180.00510.09050.0957-00.1416-0.00130.00980.17880.00280.1281-37.590218.74251.868
100.4464-0.08530.23380.058-0.00460.1712-0.0639-0.18020.26250.0460.0797-0.25080.0737-0.168-00.27320.0447-0.08640.4055-0.08410.3874-6.535938.853237.5422
111.01780.6832-0.36240.3225-0.45460.2433-0.09870.07480.05950.07310.0117-0.07420.0015-0.013300.1267-0.0091-0.0050.1793-0.00440.2137-17.055229.855522.0881
120.75320.3092-0.2490.2776-0.07530.65940.0678-0.0296-0.02420.06260.0574-0.1010.06490.02400.22440.0168-0.00220.1825-0.00020.1671-27.844913.135835.7373
130.0330.1250.0512-0.02590.08060.0169-0.02060.364-0.70760.2255-0.1418-0.1806-0.3558-0.48700.23930.0020.07230.22170.01240.28-38.541610.041647.7402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 173:184)
2X-RAY DIFFRACTION2(chain A and resid 185:201)
3X-RAY DIFFRACTION3(chain A and resid 202:214)
4X-RAY DIFFRACTION4(chain A and resid 215:221)
5X-RAY DIFFRACTION5(chain A and resid 222:266)
6X-RAY DIFFRACTION6(chain A and resid 267:278)
7X-RAY DIFFRACTION7(chain A and resid 279:308)
8X-RAY DIFFRACTION8(chain A and resid 309:331)
9X-RAY DIFFRACTION9(chain A and resid 332:363)
10X-RAY DIFFRACTION10(chain B and resid 183:217)
11X-RAY DIFFRACTION11(chain B and resid 218:294)
12X-RAY DIFFRACTION12(chain B and resid 295:356)
13X-RAY DIFFRACTION13(chain B and resid 357:367)

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