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- EMDB-3024: Structure of the type IV pilus from Thermus thermophilus -

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Basic information

Entry
Database: EMDB / ID: EMD-3024
TitleStructure of the type IV pilus from Thermus thermophilus
Map dataSubtomogram average of the Thermus thermophilus type IV pilus.
Sample
  • Sample: Type IV pilus
  • Protein or peptide: Type IV pilus
KeywordsElectron cryo-tomography / subtomogram averaging / type IV pilus / DNA transporter / bacterial secretion / T. thermophilus
Biological speciesThermus thermophilus HB27 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 Å
AuthorsGold VAM / Salzer R / Averhoff B / Kuehlbrandt W
CitationJournal: Elife / Year: 2015
Title: Structure of a type IV pilus machinery in the open and closed state.
Authors: Vicki A M Gold / Ralf Salzer / Beate Averhoff / Werner Kühlbrandt /
Abstract: Proteins of the secretin family form large macromolecular complexes, which assemble in the outer membrane of Gram-negative bacteria. Secretins are major components of type II and III secretion ...Proteins of the secretin family form large macromolecular complexes, which assemble in the outer membrane of Gram-negative bacteria. Secretins are major components of type II and III secretion systems and are linked to extrusion of type IV pili (T4P) and to DNA uptake. By electron cryo-tomography of whole Thermus thermophilus cells, we determined the in situ structure of a T4P molecular machine in the open and the closed state. Comparison reveals a major conformational change whereby the N-terminal domains of the central secretin PilQ shift by ~30 Å, and two periplasmic gates open to make way for pilus extrusion. Furthermore, we determine the structure of the assembled pilus.
History
DepositionMay 21, 2015-
Header (metadata) releaseJun 10, 2015-
Map releaseJun 10, 2015-
UpdateJun 10, 2015-
Current statusJun 10, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 143.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 143.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3024.tif

Downloads & links

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Map

FileDownload / File: emd_3024.map.gz / Format: CCP4 / Size: 188.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the Thermus thermophilus type IV pilus.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.21 Å/pix.
x 35 pix.
= 147.315 Å		4.21 Å/pix.
x 40 pix.
= 168.36 Å		4.21 Å/pix.
x 35 pix.
= 147.315 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.209 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 143.300000000000011 / Movie #1: 143.3
Minimum - Maximum136.0 - 147.0
Average (Standard dev.)140.528198239999995 (±1.21712947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-3
Dimensions403535
Spacing403535
CellA: 147.315 Å / B: 168.36 Å / C: 147.315 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.2094.2094.209
M x/y/z354035
origin x/y/z0.0000.0000.000
length x/y/z147.315168.360147.315
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00-3
NC/NR/NS354035
D min/max/mean136.000147.000140.528

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Supplemental data

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Sample components

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Entire : Type IV pilus

EntireName: Type IV pilus
Components
  • Sample: Type IV pilus
  • Protein or peptide: Type IV pilus

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Supramolecule #1000: Type IV pilus

SupramoleculeName: Type IV pilus / type: sample / ID: 1000
Oligomeric state: Thousands of copies of PilA4 form the type IV pilus
Number unique components: 1

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Macromolecule #1: Type IV pilus

MacromoleculeName: Type IV pilus / type: protein_or_peptide / ID: 1 / Name.synonym: T4P / Recombinant expression: No
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris, 100 mM EDTA
GridDetails: 300 mesh copper grid with quantifoil support film (R2/2), glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 20 % / Instrument: HOMEMADE PLUNGER
Method: Cell solutions were mixed 1:1 (v/v) with 10 nm ProteinA-gold particles. 3 microlitres of sample were applied to grids and blotted on one side for ~5s before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected on the K2 camera at magnification used for imaging
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateDec 17, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Average electron dose: 140 e/Å2
Details: Each image in every tilt series is a drift corrected sum of 3-5 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 11640 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsSubvolumes of 2 nm length were selected along the pili
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: IMOD, (ETOMO, &, PEET), Spider / Number subtomograms used: 740
CTF correctionDetails: CTF correction of each tilt image using IMOD

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