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- EMDB-1871: Three-dimensional model of Salmonella's needle complex at subnano... -

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Basic information

Entry
Database: EMDB / ID: EMD-1871
TitleThree-dimensional model of Salmonella's needle complex at subnanometer resolution
Map dataThis in an image of a the surface rendered, extracted volume of the lower neck (15 fold) of the needle complex of the type III secretion system from Salmonella tyhpimurium.
Sample
  • Sample: Needle complex from Salmonella typhimurium
  • Protein or peptide: Protein invG
KeywordsType III secretion system / Salmonella / outer membrane ring / secretin family / C15 fold
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 / protein secretion / 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
SPI-1 type 3 secretion system secretin
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 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
DepositionJan 31, 2011-
Header (metadata) releaseFeb 17, 2011-
Map releaseMar 11, 2011-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / 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-2y9k
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1871.jpg

Downloads & links

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Map

FileDownload / File: emd_1871.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis in an image of a the surface rendered, extracted volume of the lower neck (15 fold) of the needle complex of the type III secretion system from Salmonella tyhpimurium.
Voxel sizeX=Y=Z: 1.33 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.230572 - 0.204897
Average (Standard dev.)-0.000210183 (±0.0104328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 399 Å
α=β=γ: 90 °

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-0.2310.205-0.000

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Supplemental data

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Sample components

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Entire : Needle complex from Salmonella typhimurium

EntireName: Needle complex from Salmonella typhimurium
Components
  • Sample: Needle complex from Salmonella typhimurium
  • Protein or peptide: Protein invG

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Supramolecule #1000: Needle complex from Salmonella typhimurium

SupramoleculeName: Needle complex from Salmonella typhimurium / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Protein invG

MacromoleculeName: Protein invG / type: protein_or_peptide / ID: 1 / Name.synonym: invG / Recombinant expression: No
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 93000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingDigitization - Sampling interval: 15 µm / Bits/pixel: 8
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Micrograph
Final reconstructionApplied symmetry - Point group: C15 (15 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC

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Atomic model buiding 1

Initial modelPDB ID:

3gr5


Chain - Chain ID: A
DetailsProtocol: Rigid body. Based on the homolog EscC (PDB entry above) a model was built for InvG (Swissprot - template based modeling), which was subsequently used for the fitting experiment (rigid body, Software CHIMERA)
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2y9k:
Three-dimensional model of Salmonella's needle complex at subnanometer resolution

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