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- PDB-5wk6: Cryo-EM structure of P. aeruginosa flagellar filaments G420A -

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Basic information

Entry
Database: PDB / ID: 5wk6
TitleCryo-EM structure of P. aeruginosa flagellar filaments G420A
ComponentsB-type flagellin
KeywordsPROTEIN FIBRIL / bacteria flagella / helical polymers / cryo-EM
Function / homologyFlagellin / Flagellin, D0/D1 domain / Flagellin hook, IN motif / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region / Flagellin hook IN motif / bacterial-type flagellum filament / bacterial-type flagellum organization / bacterial-type flagellum-dependent cell motility / structural molecule activity ...Flagellin / Flagellin, D0/D1 domain / Flagellin hook, IN motif / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region / Flagellin hook IN motif / bacterial-type flagellum filament / bacterial-type flagellum organization / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / B-type flagellin
Function and homology information
Specimen sourcePseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / cryo EM / 4.3 Å resolution
AuthorsWang, F. / Postel, S. / Sundberg, E.J. / Egelman, E.H.
CitationJournal: Nat Commun / Year: 2017
Title: A structural model of flagellar filament switching across multiple bacterial species.
Authors: Fengbin Wang / Andrew M Burrage / Sandra Postel / Reece E Clark / Albina Orlova / Eric J Sundberg / Daniel B Kearns / Edward H Egelman
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 24, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 1, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Movie
  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-type flagellin
B: B-type flagellin
C: B-type flagellin
D: B-type flagellin
E: B-type flagellin
F: B-type flagellin
G: B-type flagellin
H: B-type flagellin
I: B-type flagellin
J: B-type flagellin
K: B-type flagellin
L: B-type flagellin
M: B-type flagellin
N: B-type flagellin
O: B-type flagellin
P: B-type flagellin
Q: B-type flagellin
R: B-type flagellin
S: B-type flagellin
T: B-type flagellin
U: B-type flagellin
V: B-type flagellin
W: B-type flagellin
X: B-type flagellin
Y: B-type flagellin
Z: B-type flagellin
a: B-type flagellin
b: B-type flagellin
c: B-type flagellin
d: B-type flagellin
e: B-type flagellin
f: B-type flagellin
g: B-type flagellin
h: B-type flagellin
i: B-type flagellin
j: B-type flagellin
k: B-type flagellin
l: B-type flagellin
m: B-type flagellin
n: B-type flagellin
o: B-type flagellin


Theoretical massNumber of molelcules
Total (without water)2,020,84441
Polyers2,020,84441
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)275580
ΔGint (kcal/M)-870
Surface area (Å2)372730
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 20 / Rise per n subunits: 4.73 Å / Rotation per n subunits: 65.27 deg.

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Components

#1: Protein/peptide ...
B-type flagellin


Mass: 49288.883 Da / Num. of mol.: 41 / Mutation: G420A
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: fliC, PA1092 / Production host: Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P72151

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Pseudomonas aeruginosa flagella filament / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Buffer solutionDetails: PBS / pH: 7.4
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: negative stain
VitrificationCryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 2 sec. / Electron dose: 20 e/Å2
Details: Images were stored containing seven parts, where each part represented a set of frames corresponding to a dose of ~20 electrons per Angstrom^2. The full dose image stack was used for the estimation of the CTF as well as for boxing filaments. Only the first two parts were used for the reconstruction (~5 electrons per Angstrom^2).
Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: dev_2439: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7Rosettamodel fitting
9SPIDERinitial Euler assignment
10SPIDERfinal Euler assignment
11SPIDERclassification
12SPIDER3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.27 deg. / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: OTHER / Number of particles: 17450 / Algorithm: BACK PROJECTION / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010161352
ELECTRON MICROSCOPYf_angle_d1.357289902
ELECTRON MICROSCOPYf_dihedral_angle_d6.96882332
ELECTRON MICROSCOPYf_chiral_restr0.05513735
ELECTRON MICROSCOPYf_plane_restr0.00627902

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