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- PDB-9ewx: Cryo-EM structure of the Pseudomonas aeruginosa PAO1 Type IV pilus -

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Basic information

Entry
Database: PDB / ID: 9ewx
TitleCryo-EM structure of the Pseudomonas aeruginosa PAO1 Type IV pilus
ComponentsPilin
KeywordsCELL ADHESION / Type IV pilus
Function / homologyFimbrial protein pilin / Pilin (bacterial filament) / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / cell adhesion / membrane / Pilin
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsOchner, H. / Boehning, J. / Wang, Z. / Tarafder, A. / Caspy, I. / Bharat, T.A.M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust225317/Z/22/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/31 United Kingdom
Engineering and Physical Sciences Research CouncilEP/V026623/1 United Kingdom
The Lister Institute of Preventive MedicineLister Prize United Kingdom
CitationJournal: To Be Published
Title: Structure of the Pseudomonas aeruginosa PAO1 Type-IV pilus
Authors: Ochner, H. / Boehning, J. / Wang, Z. / Tarafder, A. / Caspy, I. / Bharat, T.A.M.
History
DepositionApr 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilin
B: Pilin
C: Pilin
D: Pilin
E: Pilin
F: Pilin
G: Pilin
H: Pilin
I: Pilin
J: Pilin
K: Pilin
L: Pilin
M: Pilin
N: Pilin
O: Pilin
P: Pilin
Q: Pilin
R: Pilin
S: Pilin
T: Pilin
U: Pilin
V: Pilin
W: Pilin


Theoretical massNumber of molelcules
Total (without water)342,21423
Polymers342,21423
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Pilin /


Mass: 14878.889 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q5DVX0

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pseudomonas aeruginosa PAO1 Type IV Pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.015 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Buffer solutionpH: 7.5 / Details: 50 mM Tris pH 7.5, 150 mM NaCl
SpecimenConc.: 6.46 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 6.66 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5679

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 87.39 ° / Axial rise/subunit: 10.17 Å / Axial symmetry: C1
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114537 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00224311
ELECTRON MICROSCOPYf_angle_d0.39733143
ELECTRON MICROSCOPYf_dihedral_angle_d3.1413429
ELECTRON MICROSCOPYf_chiral_restr0.0444186
ELECTRON MICROSCOPYf_plane_restr0.0034209

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