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- PDB-6f2d: A FliPQR complex forms the core of the Salmonella type III secret... -

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Basic information

Entry
Database: PDB / ID: 6f2d
TitleA FliPQR complex 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 / homologyType III secretion system inner membrane P protein / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Flagellar transport protein FliP / Flagella transport protein fliP family signature 1. / Flagellar biosynthesis protein FliR / Flagellar biosynthesis protein FliQ / FliP family ...Type III secretion system inner membrane P protein / Bacterial export proteins, family 3 / Flagella transport protein fliP family signature 2. / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Flagellar transport protein FliP / Flagella transport protein fliP family signature 1. / Flagellar biosynthesis protein FliR / Flagellar biosynthesis protein FliQ / FliP family / Bacterial export proteins, family 1 / bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein targeting / protein secretion / intracellular / integral component of membrane / plasma membrane / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FliR
Function and homology information
Specimen sourceSalmonella enterica subsp. enterica (bacteria)
Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsJohnson, S. / Kuhlen, L. / Abrusci, P. / Lea, S.M.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 24, 2017 / Release: Jul 4, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 4, 2018Structure modelrepositoryInitial release
1.1Jul 18, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
1.2Jul 25, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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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
Polyers205,34110
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)38740
ΔGint (kcal/M)-497
Surface area (Å2)76400
MethodPISA

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Components

#1: Protein/peptide
Flagellar biosynthetic protein FliP


Mass: 26769.021 Da / Num. of mol.: 5
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
Details: Residues 265 onwards constitute the Twin-Strep tag used for purification
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: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliQ, flaQ, STY2188, t0897 / Production host: Escherichia coli (E. coli) / Strain (production host): Mt56 / References: UniProt: P0A1L6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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
MicroscopyMicroscope model: 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 / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging IDElectron doseDetector modeFilm or detector modelNumber of real images
1147COUNTINGGATAN K2 SUMMIT (4k x 4k)401
2150.0COUNTINGFEI FALCON III (4k x 4k)1687

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatchparticle selection
4CTFFIND4.1.8CTF correction
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
13RELION2.03D reconstruction
Image processingDetails: Images from K2 were also added.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 97718 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01012820
ELECTRON MICROSCOPYf_angle_d1.17517476
ELECTRON MICROSCOPYf_dihedral_angle_d6.61510451
ELECTRON MICROSCOPYf_chiral_restr0.0542189
ELECTRON MICROSCOPYf_plane_restr0.0082130

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