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- EMDB-1874: Three-dimensional model of Salmonella's needle complex at subnano... -

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Basic information

Entry
Database: EMDB / ID: EMD-1874
TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution
Map dataThis in an image of a surface rendered, extracted volume of the IR1 from the needle complex from Salmonella typhimurium
Sample
  • Sample: Needle complex of the type III secretion system from Salmonella typhimurium - periplasmic domain of the inner membrane associated ring IR1
  • Protein or peptide: Protein PrgH
  • Protein or peptide: Protein PrgK
Keywordstype III secretion / IR1 / inner membrane ring / C24-fold
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: 6.4 Å
AuthorsSchraidt O / Marlovits TC
CitationJournal: Science / Year: 2011
Title: Three-dimensional model of Salmonella's needle complex at subnanometer resolution.
Authors: Oliver Schraidt / Thomas C Marlovits /
Abstract: Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core ...Type III secretion systems (T3SSs) are essential virulence factors used by many Gram-negative bacteria to inject proteins that make eukaryotic host cells accessible to invasion. The T3SS core structure, the needle complex (NC), is a ~3.5 megadalton-sized, oligomeric, membrane-embedded complex. Analyzing cryo-electron microscopy images of top views of NCs or NC substructures from Salmonella typhimurium revealed a 24-fold symmetry for the inner rings and a 15-fold symmetry for the outer rings, giving an overall C3 symmetry. Local refinement and averaging showed the organization of the central core and allowed us to reconstruct a subnanometer composite structure of the NC, which together with confident docking of atomic structures reveal insights into its overall organization and structural requirements during assembly.
History
DepositionFeb 10, 2011-
Header (metadata) releaseFeb 17, 2011-
Map releaseMar 11, 2011-
UpdateNov 26, 2014-
Current statusNov 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.076
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.076
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2y9j
  • Surface level: 0.076
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1874.jpg

Downloads & links

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Map

FileDownload / File: emd_1874.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis in an image of a surface rendered, extracted volume of the IR1 from the needle complex from Salmonella typhimurium
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 300 pix.
= 399. Å		1.33 Å/pix.
x 300 pix.
= 399. Å		1.33 Å/pix.
x 300 pix.
= 399. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.33 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.076 / Movie #1: 0.076
Minimum - Maximum-0.18737172 - 0.21286634
Average (Standard dev.)0.0002095 (±0.01604983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 399.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.331.331.33
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z399.000399.000399.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-0.1870.2130.000

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Supplemental data

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Sample components

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Entire : Needle complex of the type III secretion system from Salmonella t...

EntireName: Needle complex of the type III secretion system from Salmonella typhimurium - periplasmic domain of the inner membrane associated ring IR1
Components
  • Sample: Needle complex of the type III secretion system from Salmonella typhimurium - periplasmic domain of the inner membrane associated ring IR1
  • Protein or peptide: Protein PrgH
  • Protein or peptide: Protein PrgK

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Supramolecule #1000: Needle complex of the type III secretion system from Salmonella t...

SupramoleculeName: Needle complex of the type III secretion system from Salmonella typhimurium - periplasmic domain of the inner membrane associated ring IR1
type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 2

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Macromolecule #1: Protein PrgH

MacromoleculeName: Protein PrgH / type: protein_or_peptide / ID: 1 / Name.synonym: Protein PrgH / Oligomeric state: 24mer / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Location in cell: Membrane

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Macromolecule #2: Protein PrgK

MacromoleculeName: Protein PrgK / type: protein_or_peptide / ID: 2 / Name.synonym: Protein PrgK / Oligomeric state: 24mer / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Location in cell: Membrane

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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 / Details: 10mM Tris-HCl, 0.5M NaCl, 0.1% LDAO
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingDigitization - Sampling interval: 15 µm / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Micrograph
Final reconstructionApplied symmetry - Point group: C24 (24 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC

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Atomic model buiding 1

Initial modelPDB ID:

1yj7

SoftwareName: Chimera
DetailsProtocol: Rigid Body. Based on the homolog EscJ (PDB entry above) a model was built for PrgK (Swissmodel) which was subsequently used for the fitting experiment (rigid body, Chimera), each chain was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-2y9j:
THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANOMETER RESOLUTION

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Atomic model buiding 2

Initial modelPDB ID:

3gr1

SoftwareName: Chimera
DetailsProtocol: Rigid Body. Each chain was fitted separately
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-2y9j:
THREE-DIMENSIONAL MODEL OF SALMONELLA'S NEEDLE COMPLEX AT SUBNANOMETER RESOLUTION

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