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- PDB-6xxd: CryoEM structure of the type IV pilin PilA4 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 6xxd
TitleCryoEM structure of the type IV pilin PilA4 from Thermus thermophilus
ComponentsPilA
KeywordsCELL ADHESION / Type IV pilin glycosylation twitching motility
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / cell outer membrane / periplasmic space / membrane => GO:0016020 / 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 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsNeuhaus, A. / Gold, V.A.M.
Funding support United Kingdom, 1items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

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Assembly

Deposited unit
A: PilA
B: PilA
C: PilA
D: PilA
E: PilA
F: PilA
G: PilA
H: PilA
I: PilA
J: PilA
K: PilA
L: PilA
M: PilA
N: PilA
O: PilA
P: PilA


Theoretical massNumber of molelcules
Total (without water)212,01816
Polymers212,01816
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area53910 Å2
ΔGint-410 kcal/mol
Surface area71050 Å2
MethodPISA

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Components

#1: Protein
PilA


Mass: 13251.123 Da / Num. of mol.: 16 / Source method: isolated from a natural source
Details: Sequence corresponds to the mature protein. The first 6 residues are removed by prepilin peptidase.
Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
References: UniProt: Q72JC0

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Thermus thermophilus wide pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Thermus thermophilus HB27 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 47.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 92.5 ° / Axial rise/subunit: 9.33 Å / Axial symmetry: C1
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65656 / Symmetry type: HELICAL

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