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- EMDB-41298: CryoEM structure of Myxococcus xanthus type IV pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-41298
TitleCryoEM structure of Myxococcus xanthus type IV pilus
Map data
Sample
  • Complex: Myxococcus xanthus type IV pilus
    • Protein or peptide: Type IV major pilin protein PilA
Keywordsfilament / helical reconstruction / CryoEM / CELL ADHESION
Function / homologyType IV pilin PilA / Type IV pilin PilA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / membrane / Type IV major pilin protein PilA
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZheng W / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: bioRxiv / Year: 2023
Title: Large pilin subunits provide distinct structural and mechanical properties for the type IV pilus.
Authors: Anke Treuner-Lange / Weili Zheng / Albertus Viljoen / Steffi Lindow / Marco Herfurth / Yves F Dufrêne / Lotte Søgaard-Andersen / Edward H Egelman
Abstract: Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built ...Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While the major pilins of structurally characterized T4P have lengths of up to 161 residues, the major pilin PilA of is unusually large with 208 residues. All major pilins have a highly conserved N-terminal domain and a highly variable C-terminal domain, and the additional residues in the PilA are due to a larger C-terminal domain. We solved the structure of the T4P (T4P ) at a resolution of 3.0 Å using cryo-electron microscopy (cryo-EM). The T4P follows the structural blueprint observed in other T4P with the pilus core comprised of the extensively interacting N-terminal α1-helices while the globular domains decorate the T4P surface. The atomic model of PilA built into this map shows that the large C-terminal domain has much more extensive intersubunit contacts than major pilins in other T4P. As expected from these greater contacts, the bending and axial stiffness of the T4P is significantly higher than that of other T4P and supports T4P-dependent motility on surfaces of different stiffnesses. Notably, T4P variants with interrupted intersubunit interfaces had decreased bending stiffness and strongly reduced motility on all surfaces. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4P that expands the environmental conditions in which the T4P system functions.
History
DepositionJul 20, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41298.png

Downloads & links

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Map

FileDownload / File: emd_41298.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-2.4213235 - 4.064965
Average (Standard dev.)0.00749419 (±0.14990683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41298_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41298_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Myxococcus xanthus type IV pilus

EntireName: Myxococcus xanthus type IV pilus
Components
  • Complex: Myxococcus xanthus type IV pilus
    • Protein or peptide: Type IV major pilin protein PilA

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Supramolecule #1: Myxococcus xanthus type IV pilus

SupramoleculeName: Myxococcus xanthus type IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)

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Macromolecule #1: Type IV major pilin protein PilA

MacromoleculeName: Type IV major pilin protein PilA / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Myxococcus xanthus DK 1622 (bacteria)
Molecular weightTheoretical: 21.932318 KDa
SequenceString: FTLIELMIVV AIIGILAAIA IPNFIKFQAR SKQSEAKTNL KALYTAQKSF FSEKDRYSDF ANEIGFAPER GNRYGYRVSA AAGDCEVRN AADLPVPAAG VPCISNDSFR FGANSAIDDP TPVVARFVPQ GAAGWNTTLG VQPTIADCPN CNFFAGARGN A DNEATFDD ...String:
FTLIELMIVV AIIGILAAIA IPNFIKFQAR SKQSEAKTNL KALYTAQKSF FSEKDRYSDF ANEIGFAPER GNRYGYRVSA AAGDCEVRN AADLPVPAAG VPCISNDSFR FGANSAIDDP TPVVARFVPQ GAAGWNTTLG VQPTIADCPN CNFFAGARGN A DNEATFDD WVIAGFEGSG QVGPCSEAGN VASGTPYNTR NDVACDGAAQ

UniProtKB: Type IV major pilin protein PilA

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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: 7.5
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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Helical parameters - Δz: 10.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 100.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1300000

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