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- EMDB-10647: CryoEM structure of the wide type IV pilus (PilA4) from Thermus t... -

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Basic information

Entry
Database: EMDB / ID: EMD-10647
TitleCryoEM structure of the wide type IV pilus (PilA4) from Thermus thermophilus
Map data
Sample
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: PilA
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / membrane => GO:0016020 / periplasmic space / plasma membrane
Similarity search - Function
Bacterial general secretion pathway protein G-type pilin / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site
Similarity search - Domain/homology
Type IV wide pilus major component PilA4
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsNeuhaus A / Gold VAM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R008639/1 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium.
Authors: Alexander Neuhaus / Muniyandi Selvaraj / Ralf Salzer / Julian D Langer / Kerstin Kruse / Lennart Kirchner / Kelly Sanders / Bertram Daum / Beate Averhoff / Vicki A M Gold /
Abstract: Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm ...Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility.
History
DepositionJan 27, 2020-
Header (metadata) releaseFeb 5, 2020-
Map releaseMar 11, 2020-
UpdateMay 20, 2020-
Current statusMay 20, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xxd
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10647.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 5 / Movie #1: 5
Minimum - Maximum-6.239147 - 22.136034
Average (Standard dev.)-0.0000000087 (±0.9999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 167.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z167.680167.680167.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-6.23922.136-0.000

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Supplemental data

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Sample components

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Entire : Thermus thermophilus wide pilus

EntireName: Thermus thermophilus wide pilus
Components
  • Complex: Thermus thermophilus wide pilus
    • Protein or peptide: PilA

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Supramolecule #1: Thermus thermophilus wide pilus

SupramoleculeName: Thermus thermophilus wide pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)

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Macromolecule #1: PilA

MacromoleculeName: PilA / type: protein_or_peptide / ID: 1
Details: Sequence corresponds to the mature protein. The first 6 residues are removed by prepilin peptidase.
Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Molecular weightTheoretical: 13.251123 KDa
SequenceString:
FTLIELLIVI AIIAILAAVL IPNLLAARKR ANDTVVTAYL NDAVKFQEMY QIDNNSYTSN QAALISLGLK STPANVTFSI VSASANSYC MIAGHSGGTV WFAATPDKGV YKTNTAVTSS QPESCP

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 47.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 9.33 Å
Applied symmetry - Helical parameters - Δ&Phi: 92.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65656
FSC plot (resolution estimation)

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