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- PDB-5wjy: Cryo-EM structure of B. subtilis flagellar filaments S285P -

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Basic information

Database: PDB / ID: 5wjy
TitleCryo-EM structure of B. subtilis flagellar filaments S285P
KeywordsPROTEIN FIBRIL / bacteria flagella / helical polymers / cryo-EM
Function / homologyFlagellin, D0/D1 domain / Flagellin / Bacterial flagellin N-terminal helical region / Bacterial flagellin C-terminal helical region / bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / Flagellin
Function and homology information
Specimen sourceBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / negative staining / cryo EM / 4.5 Å resolution
AuthorsWang, F. / Burrage, A.M. / Kearns, D.B. / 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

Structure visualization

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

Theoretical massNumber of molelcules
Total (without water)1,339,52441

  • 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)292380
ΔGint (kcal/M)-1157
Surface area (Å2)424000
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 20 / Rise per n subunits: 4.72 Å / Rotation per n subunits: 65.3 deg.


#1: Protein/peptide ...
Flagellin /

Mass: 32671.320 Da / Num. of mol.: 41 / Mutation: S285P,T209C / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3365 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A162QQD4

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

Sample preparation

ComponentName: Bacillus subtilis flagella filament / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Bacillus subtilis (bacteria)
Buffer solutionDetails: Imidazole buffer / pH: 6.8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: negative stain
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 %

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


SoftwareName: PHENIX / Version: dev_2439: / Classification: refinement
EM software
1EMAN2particle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7Rosettamodel fitting
9SPIDERinitial Euler assignment
10SPIDERfinal Euler assignment
12SPIDER3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
Helical symmertyAngular rotation/subunit: 65.3 deg. / Axial rise/subunit: 4.72 Å / Axial symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: OTHER / Number of particles: 55403 / Algorithm: BACK PROJECTION / Details: model-map FSC 0.38 cut-off / Symmetry type: HELICAL
Atomic model buildingRef space: REAL
Least-squares processHighest resolution: 4.5 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006185443
ELECTRON MICROSCOPYf_angle_d1.239334929
ELECTRON MICROSCOPYf_dihedral_angle_d9.48473226
ELECTRON MICROSCOPYf_chiral_restr0.05614965
ELECTRON MICROSCOPYf_plane_restr0.00431447

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