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- EMDB-5722: Structure of the trypsin-resistant core of secretin YscC -

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Basic information

Entry
Database: EMDB / ID: EMD-5722
TitleStructure of the trypsin-resistant core of secretin YscC
Map dataReconstruction of the trypsin-resistant core of YscC
Sample
  • Sample: Trypsinized YscC secretin from Yersinia enterocolitica
  • Protein or peptide: YscC secretin, trypsin-treated
Keywordstype III secretion system / Yersinia enterocolitica / Gram-negative bacteria / YscC / secretin / cryo-electron microscopy / outer membrane / trypsin-resistant core
Function / homology
Function and homology information


type III protein secretion system complex / protein secretion by the type III secretion system / cell outer membrane / identical protein binding
Similarity search - Function
: / SPI-1 type 3 secretion system secretin, N0 domain / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein
Similarity search - Domain/homology
Type 3 secretion system secretin
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsKowal J / Chami M / Ringler P / Muller AS / Kudryashev M / Castano-Diez D / Amstutz M / Cornelis GR / Stahlberg H / Engel A
CitationJournal: Structure / Year: 2013
Title: Structure of the dodecameric Yersinia enterocolitica secretin YscC and its trypsin-resistant core.
Authors: Julia Kowal / Mohamed Chami / Philippe Ringler / Shirley A Müller / Mikhail Kudryashev / Daniel Castaño-Díez / Marlise Amstutz / Guy R Cornelis / Henning Stahlberg / Andreas Engel /
Abstract: The type III secretion system machinery, also known as the injectisome, delivers bacterial effector proteins into eukaryotic cells during infection. The outer membrane YscC secretin is a major part ...The type III secretion system machinery, also known as the injectisome, delivers bacterial effector proteins into eukaryotic cells during infection. The outer membrane YscC secretin is a major part of Yersinia enterocolitica's injectisome and is among the first components to assemble, solely assisted by its pilotin, YscW. We have determined the three-dimensional structures of the native complex and its protease-resistant core to 12 Å resolution by cryo-electron microscopy (cryo-EM) and show that YscC forms a dodecameric complex. Cryo-EM of YscC reconstituted into proteoliposomes defines the secretin's membrane-spanning region. Native YscC consists of an outer membrane ring connected via a thin cylindrical wall to a conical, periplasmic region that exposes N-terminal petals connected by flexible linkers. These petals harbor the binding site of YscD, a component of the inner membrane ring. A change in their orientation adapts the length of the YscC secretin and facilitates its interaction with YscD.
History
DepositionJul 17, 2013-
Header (metadata) releaseNov 13, 2013-
Map releaseNov 13, 2013-
UpdateDec 18, 2013-
Current statusDec 18, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.031
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.031
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5722.png

Downloads & links

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Map

FileDownload / File: emd_5722.map.gz / Format: CCP4 / Size: 12.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the trypsin-resistant core of YscC
Voxel sizeX=Y=Z: 1.95 Å
Density
Contour LevelBy AUTHOR: 0.031 / Movie #1: 0.031
Minimum - Maximum-0.07850298 - 0.08096476
Average (Standard dev.)0.0001529 (±0.01168504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-74-74-74
Dimensions148148148
Spacing148148148
CellA=B=C: 288.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.951.951.95
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z288.600288.600288.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-74-74-74
NC/NR/NS148148148
D min/max/mean-0.0790.0810.000

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Supplemental data

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Sample components

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Entire : Trypsinized YscC secretin from Yersinia enterocolitica

EntireName: Trypsinized YscC secretin from Yersinia enterocolitica
Components
  • Sample: Trypsinized YscC secretin from Yersinia enterocolitica
  • Protein or peptide: YscC secretin, trypsin-treated

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Supramolecule #1000: Trypsinized YscC secretin from Yersinia enterocolitica

SupramoleculeName: Trypsinized YscC secretin from Yersinia enterocolitica
type: sample / ID: 1000 / Details: Sample contained detergent DDM / Oligomeric state: 12 / Number unique components: 1
Molecular weightTheoretical: 384 KDa

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Macromolecule #1: YscC secretin, trypsin-treated

MacromoleculeName: YscC secretin, trypsin-treated / type: protein_or_peptide / ID: 1
Details: Purified YscC oligomer was incubated with N-p-tosyl-L-phenylalanine chloromethyl ketone-treated trypsin (Sigma) for 2 h at room temperature.
Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Organism: Yersinia enterocolitica (bacteria) / Strain: W22703 / synonym: Yersinia / Location in cell: outer membrane
Molecular weightTheoretical: 384 KDa
Recombinant expressionOrganism: Yersinia enterocolitica (bacteria) / Recombinant strain: W22703 / Recombinant plasmid: pMA6, pRS6
SequenceUniProtKB: Type 3 secretion system secretin

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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

Concentration0.1 mg/mL
BufferpH: 7.8
Details: 10 mM Tris-HCl, 100 mM NaCl, 0.1 mM EDTA, 0.04% DDM
GridDetails: 200 mesh Cu grid, covered with a very thin additional continuous carbon film, glow-discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV / Method: Plunging immediately after blotting.

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateOct 2, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5 µm / Number real images: 80 / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: each particle
Final two d classificationNumber classes: 127
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 13000
DetailsParticles were selected using Boxer/EMAN1.9. Image processing was done using EMAN2.

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