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- EMDB-1160: Double hexameric ring assembly of the type III protein translocas... -

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Basic information

Entry
Database: EMDB / ID: EMD-1160
TitleDouble hexameric ring assembly of the type III protein translocase ATPase HrcN.
Map dataThis volume contains the 3D reconstruction of dodecameric HrcN. It is D6-symmetrized. A threshold of 0.61 is recommended for surface rendering.
Sample
  • Sample: HrcN
  • Protein or peptide: HrcN
Biological speciesPseudomonas syringae pv. phaseolicola (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsMuller SA / Poyidis C / Stone R / Meesters C / Chami M / Engel A / Economou A / Stahlberg H
CitationJournal: Mol Microbiol / Year: 2006
Title: Double hexameric ring assembly of the type III protein translocase ATPase HrcN.
Authors: Shirley A Müller / Charalambos Pozidis / Remington Stone / Christian Meesters / Mohamed Chami / Andreas Engel / Anastassios Economou / Henning Stahlberg /
Abstract: The specialized type III secretion (T3S) apparatus of pathogenic and symbiotic Gram-negative bacteria comprises a complex transmembrane organelle and an ATPase homologous to the F1-ATPase beta ...The specialized type III secretion (T3S) apparatus of pathogenic and symbiotic Gram-negative bacteria comprises a complex transmembrane organelle and an ATPase homologous to the F1-ATPase beta subunit. The T3S ATPase HrcN of Pseudomonas syringae associates with the inner membrane, and its ATP hydrolytic activity is stimulated by dodecamerization. The structure of dodecameric HrcN (HrcN12) determined to 1.6 nm by cryo-electron microscopy is presented. HrcN12 comprises two hexameric rings that are probably stacked face-to-face by the association of their C-terminal domains. It is 11.5 +/- 1.0 nm in diameter, 12.0 +/- 2.0 nm high and has a 2.0-3.8 nm wide inner channel. This structure is compared to a homology model based on the structure of the F1-beta-ATPase. A model for its incorporation within the T3S apparatus is presented.
History
DepositionSep 22, 2005-
Header (metadata) releaseSep 22, 2005-
Map releaseAug 7, 2006-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.61
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.61
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1160.gif

Downloads & links

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Map

FileDownload / File: emd_1160.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis volume contains the 3D reconstruction of dodecameric HrcN. It is D6-symmetrized. A threshold of 0.61 is recommended for surface rendering.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 100 pix.
= 400. Å		4 Å/pix.
x 100 pix.
= 400. Å		4 Å/pix.
x 100 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.802 / Movie #1: 0.61
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.226394 (±0.22867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 400 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean0.0001.0000.226

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Supplemental data

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Sample components

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Entire : HrcN

EntireName: HrcN
Components
  • Sample: HrcN
  • Protein or peptide: HrcN

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Supramolecule #1000: HrcN

SupramoleculeName: HrcN / type: sample / ID: 1000
Details: The sample had a tendency to aggregate rapidly. Images were usually highly crowded, or empty, from the same cryo-EM grid.
Oligomeric state: homododecamer / Number unique components: 1
Molecular weightExperimental: 601 KDa / Theoretical: 612 KDa / Method: STEM mass measurement

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Macromolecule #1: HrcN

MacromoleculeName: HrcN / type: protein_or_peptide / ID: 1 / Name.synonym: HrcN / Number of copies: 12 / Oligomeric state: dodecamer / Recombinant expression: Yes
Source (natural)Organism: Pseudomonas syringae pv. phaseolicola (bacteria) / synonym: Pseudomonas syringae pathovar phaseolicola
Molecular weightExperimental: 612 KDa / Theoretical: 601 KDa

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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

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 50mM Tris-Cl, pH 7.4, 0.2M NaCl, 20% glycerol
GridDetails: Quantifoil 300 mesh
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home-built

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingDigitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5.0 µm / Number real images: 165 / Od range: 1 / Bits/pixel: 16
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: SPIDER
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 8742
Final two d classificationNumber classes: 352

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