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- EMDB-20833: Cryo-EM reconstruction of the PrgHK periplasmic ring from Salmone... -

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Basic information

Entry
Database: EMDB / ID: EMD-20833
TitleCryo-EM reconstruction of the PrgHK periplasmic ring from Salmonella's needle complex assembled in the absence of the export apparatus
Map data
Sample
  • Complex: Complex of the periplasmic domains of PrgH and PrgK from Salmonella's needle complex assembled in the absence of the export apparatus
    • Protein or peptide: Lipoprotein PrgK
    • Protein or peptide: Protein PrgH
KeywordsBACTERIAL NANOMACHINE / TYPE III SECRETION SYSTEM / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
Type III secretion system, PrgH/EprH / Type III secretion system lipoprotein HrcJ/YscJ / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Protein PrgH / Lipoprotein PrgK
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsButan C / Galan J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: High-resolution view of the type III secretion export apparatus in situ reveals membrane remodeling and a secretion pathway.
Authors: Carmen Butan / Maria Lara-Tejero / Wenwei Li / Jun Liu / Jorge E Galán /
Abstract: Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into ...Type III protein secretion systems are essential virulence factors for many important pathogenic bacteria. The entire protein secretion machine is composed of several substructures that organize into a holostructure or injectisome. The core component of the injectisome is the needle complex, which houses the export apparatus that serves as a gate for the passage of the secreted proteins through the bacterial inner membrane. Here, we describe a high-resolution structure of the export apparatus of the type III secretion system in association with the needle complex and the underlying bacterial membrane, both in isolation and in situ. We show the precise location of the core export apparatus components within the injectisome and bacterial envelope and demonstrate that their deployment results in major membrane remodeling and thinning, which may be central for the protein translocation process. We also show that InvA, a critical export apparatus component, forms a multiring cytoplasmic conduit that provides a pathway for the type III secretion substrates to reach the entrance of the export gate. Combined with structure-guided mutagenesis, our studies provide major insight into potential mechanisms of protein translocation and injectisome assembly.
History
DepositionOct 15, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseJul 1, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uov
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6uov
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20833.png

Downloads & links

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Map

FileDownload / File: emd_20833.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.06
Minimum - Maximum-0.19026065 - 0.2869908
Average (Standard dev.)0.0006777041 (±0.0117254555)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z385.200385.200385.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1900.2870.001

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Supplemental data

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Sample components

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Entire : Complex of the periplasmic domains of PrgH and PrgK from Salmonel...

EntireName: Complex of the periplasmic domains of PrgH and PrgK from Salmonella's needle complex assembled in the absence of the export apparatus
Components
  • Complex: Complex of the periplasmic domains of PrgH and PrgK from Salmonella's needle complex assembled in the absence of the export apparatus
    • Protein or peptide: Lipoprotein PrgK
    • Protein or peptide: Protein PrgH

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Supramolecule #1: Complex of the periplasmic domains of PrgH and PrgK from Salmonel...

SupramoleculeName: Complex of the periplasmic domains of PrgH and PrgK from Salmonella's needle complex assembled in the absence of the export apparatus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Lipoprotein PrgK

MacromoleculeName: Lipoprotein PrgK / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 28.245287 KDa
SequenceString: MIRRYLYTFL LVMTLAGCKD KDLLKGLDQE QANEVIAVLQ MHNIEANKID SGKLGYSITV AEPDFTAAVY WIKTYQLPPR PRVEIAQMF PADSLVSSPR AEKARLYSAI EQRLEQSLQT MEGVLSARVH ISYDIDAGEN GRPPKPVHLS ALAVYERGSP L AHQISDIK ...String:
MIRRYLYTFL LVMTLAGCKD KDLLKGLDQE QANEVIAVLQ MHNIEANKID SGKLGYSITV AEPDFTAAVY WIKTYQLPPR PRVEIAQMF PADSLVSSPR AEKARLYSAI EQRLEQSLQT MEGVLSARVH ISYDIDAGEN GRPPKPVHLS ALAVYERGSP L AHQISDIK RFLKNSFADV DYDNISVVLS ERSDAQLQAP GTPVKRNSFA TSWIVLIILL SVMSAGFGVW YYKNHYARNK KG ITADDKA KSSNE

UniProtKB: Lipoprotein PrgK

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Macromolecule #2: Protein PrgH

MacromoleculeName: Protein PrgH / type: protein_or_peptide / ID: 2 / Number of copies: 23 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 44.509367 KDa
SequenceString: METSKEKTIT SPGPYIVRLL NSSLNGCEFP LLTGRTLFVV GQSDALTASG QLPDIPADSF FIPLDHGGVN FEIQVDTDAT EIILHELKE GNSESRSVQL NTPIQVGELL ILIRPESEPW VPEQPEKLET SAKKNEPRFK NGIVAALAGF FILGIGTVGT L WILNSPQR ...String:
METSKEKTIT SPGPYIVRLL NSSLNGCEFP LLTGRTLFVV GQSDALTASG QLPDIPADSF FIPLDHGGVN FEIQVDTDAT EIILHELKE GNSESRSVQL NTPIQVGELL ILIRPESEPW VPEQPEKLET SAKKNEPRFK NGIVAALAGF FILGIGTVGT L WILNSPQR QAAELDSLLG QEKERFQVLP GRDKMLYVAA QNERDTLWAR QVLARGDYDK NARVINENEE NKRISIWLDT YY PQLAYYR IHFDEPRKPV FWLSRQRNTM SKKELEVLSQ KLRALMPYAD SVNITLMDDV TAAGQAEAGL KQQALPYSRR NHK GGVTFV IQGALDDVEI LRARQFVDSY YRTWGGRYVQ FAIELKDDWL KGRSFQYGAE GYIKMSPGHW YFPSPL

UniProtKB: Protein PrgH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C23 (23 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 10674
FSC plot (resolution estimation)

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