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- EMDB-5720: Structure of the Yersinia enterocolitica secretin YscC -

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Basic information

Entry
Database: EMDB / ID: EMD-5720
TitleStructure of the Yersinia enterocolitica secretin YscC
Map dataReconstruction of YscC secretin
Sample
  • Sample: YscC secretin from Yersinia enterocolitica
  • Protein or peptide: YscC secretin
Keywordstype III secretion system / Yersinia enterocolitica / Gram-negative bacteria / YscC / secretin / cryo-electron microscopy / outer membrane
Function / homology
Function and homology information


type III protein secretion system complex / type II 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 / NolW-like superfamily / Bacterial type II/III secretion system short domain / 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 16, 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: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.034
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5720.png

Downloads & links

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Map

FileDownload / File: emd_5720.map.gz / Format: CCP4 / Size: 12.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of YscC secretin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.95 Å/pix.
x 148 pix.
= 288.6 Å		1.95 Å/pix.
x 148 pix.
= 288.6 Å		1.95 Å/pix.
x 148 pix.
= 288.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034 / Movie #1: 0.034
Minimum - Maximum-0.14436568 - 0.11775511
Average (Standard dev.)0.0007342 (±0.0204073)
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-0.1440.1180.001

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Supplemental data

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Sample components

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Entire : YscC secretin from Yersinia enterocolitica

EntireName: YscC secretin from Yersinia enterocolitica
Components
  • Sample: YscC secretin from Yersinia enterocolitica
  • Protein or peptide: YscC secretin

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Supramolecule #1000: YscC secretin from Yersinia enterocolitica

SupramoleculeName: YscC secretin from Yersinia enterocolitica / type: sample / ID: 1000 / Details: Sample contained detergent DDM / Oligomeric state: 12 / Number unique components: 1
Molecular weightExperimental: 900 KDa / Theoretical: 768 KDa / Method: Gel filtration, Superose 6 30/100 GL column

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Macromolecule #1: YscC secretin

MacromoleculeName: YscC secretin / type: protein_or_peptide / ID: 1 / Oligomeric state: Dodecamer / Recombinant expression: Yes
Source (natural)Organism: Yersinia enterocolitica (bacteria) / Strain: W22703 / synonym: Yersinia / Location in cell: outer membrane
Molecular weightTheoretical: 768 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

Concentration0.2 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
DateOct 1, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5 µm / Number real images: 100 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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

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Image processing

DetailsParticles were selected using Boxer/EMAN1.9. Image processing was done using EMAN2.
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2
Details: Mask parameters were optimized to minimize the influence of a flexible N-terminal domain that impaired projection alignment.
Number images used: 35000
Final two d classificationNumber classes: 240

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