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- PDB-6r69: Improved map of the FliPQR complex that forms the core of the Sal... -

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Basic information

Entry
Database: PDB / ID: 6r69
TitleImproved map of the FliPQR complex that forms the core of the Salmonella type III secretion system export apparatus.
Components
  • Flagellar biosynthetic protein FliP
  • Flagellar biosynthetic protein FliQ
  • Flagellar biosynthetic protein FliR
KeywordsPROTEIN TRANSPORT / T3SS / Flagella / Cryo-EM / Export / Membrane protein
Function / homology
Function and homology information


bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein secretion / protein targeting / integral component of membrane / plasma membrane
Type III secretion system inner membrane P protein / Flagellar transport protein FliP / Bacterial export proteins, family 3 / Bacterial export proteins, family 1 / FliP family / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Bacterial export protein family 3 / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Flagella transport protein fliP family signature 1.
Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Biological speciesSalmonella enterica subsp. enterica (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Salmonella enterica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsJohnson, S. / Kuhlen, L. / Abrusci, P. / Lea, S.M.
Funding supportUnited Kingdom , 5件
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)M011984United Kingdom
Wellcome Trust100298United Kingdom
Wellcome Trust201536United Kingdom
Wolfson FoundationWL160052United Kingdom
Wellcome Trust109136United Kingdom
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structure of the core of the type III secretion system export apparatus.
Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / Carol V Robinson / Susan M Lea /
Abstract: Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are ...Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. Here, we present the cryoelectron microscopy structure of the Salmonella Typhimurium FliP-FliQ-FliR complex at 4.2 Å. None of the subunits adopt canonical integral membrane protein topologies, and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems, combined with cross-linking, localize the export gate as a core component of the periplasmic portion of the machinery. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 26, 2019 / Release: May 29, 2019
RevisionDateData content typeProviderType
1.0May 29, 2019Structure modelrepositoryInitial release

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Flagellar biosynthetic protein FliP
B: Flagellar biosynthetic protein FliP
C: Flagellar biosynthetic protein FliP
D: Flagellar biosynthetic protein FliP
E: Flagellar biosynthetic protein FliP
F: Flagellar biosynthetic protein FliR
G: Flagellar biosynthetic protein FliQ
H: Flagellar biosynthetic protein FliQ
I: Flagellar biosynthetic protein FliQ
J: Flagellar biosynthetic protein FliQ


Theoretical massNumber of molelcules
Total (without water)205,34110
Polymers205,34110
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43020 Å2
ΔGint-542 kcal/mol
Surface area69010 Å2
MethodPISA

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Components

#1: Protein/peptide
Flagellar biosynthetic protein FliP


Mass: 26769.021 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica (bacteria)
Gene: fliP, LTSERUB_0568 / Production host: Escherichia coli (E. coli) / Strain (production host): MT56 / References: UniProt: G5QE81
#2: Protein/peptide Flagellar biosynthetic protein FliR


Mass: 33069.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliR, flaP, STM1981 / Production host: Escherichia coli (E. coli) / Strain (production host): MT56 / References: UniProt: P54702
#3: Protein/peptide
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria)
Gene: fliQ, fliQ_1, fliQ_2, A7D45_07890, A7S51_18675, AL463_17545, BH006_19970, BUJ17_0011480, BUJ19_005435, C4801_20645, C4860_05670, CBI64_04070, CHC34_11945, CHD23_08750, CHE19_09990, CIC26_24535, CRE05_10505, IN95_15645, NCTC10252_03215, NCTC10718_02756, NCTC6385_02264, NCTC9854_01819
Production host: Escherichia coli (E. coli) / Strain (production host): MT56 / References: UniProt: A0A0M0QTK6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of the flagellar type III secretion system export apparatus components FliP, FliQ and FliRType three secretion system
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightValue: 195 kDa/nm / Experimental value: YES
Source (natural)Organism: Salmonella enterica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Mt56
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording

Imaging-ID: 1 / Detector mode: COUNTING

IDElectron dose (e/Å2)Film or detector modelNum. of real images
147GATAN K2 SUMMIT (4k x 4k)401
250FEI FALCON III (4k x 4k)1687

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Processing

Software

Classification: refinement / Version: dev_3406 / NB:

Name
phenix.real_space_refine
PHENIX
EM software
IDNameVersionCategory
1Gautomatchparticle selection
4CTFFIND4.1.8CTF correction
7PHENIXDEV_3406model fitting
9PHENIXDEV_3406model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
Image processingDetails: Images from K2 were also added.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97719 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6F2D
RefinementHighest resolution: 3.65 Å
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.005312820
f_angle_d0.777417476
f_chiral_restr0.04472189
f_plane_restr0.00712130
f_dihedral_angle_d3.49797731

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