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- PDB-9cef: Caulobacter crescentus FljN flagellar filament (symmetrized) -

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Basic information

Entry
Database: PDB / ID: 9cef
TitleCaulobacter crescentus FljN flagellar filament (symmetrized)
ComponentsFlagellin FljN
KeywordsSTRUCTURAL PROTEIN / flagellin / flagellar filament
Function / homologyFlagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum / structural molecule activity / extracellular region / Flagellin FljN
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsSanchez, J.C. / Montemayor, E.J. / Ploscariu, N.T. / Parrell, D. / Baumgardt, J.K. / Yang, J.E. / Sibert, B. / Cai, K. / Wright, E.R.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104540 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM139168 United States
Department of Energy (DOE, United States)DE-SC0018409 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM135066 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM143854 United States
CitationJournal: To Be Published
Title: Direct evidence for multi-flagellin filament stabilization via atomic-level architecture of Caulobacter crescentus flagellar filaments
Authors: Sanchez, J.C. / Montemayor, E.J. / Ploscariu, N.T. / Parrell, D. / Baumgardt, J.K. / Yang, J.E. / Sibert, B. / Cai, K. / Wright, E.R.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 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: Flagellin FljN
B: Flagellin FljN
C: Flagellin FljN
D: Flagellin FljN
E: Flagellin FljN
F: Flagellin FljN
G: Flagellin FljN
H: Flagellin FljN
I: Flagellin FljN
J: Flagellin FljN
K: Flagellin FljN
L: Flagellin FljN
M: Flagellin FljN
N: Flagellin FljN
O: Flagellin FljN
P: Flagellin FljN
Q: Flagellin FljN
R: Flagellin FljN
S: Flagellin FljN
T: Flagellin FljN
U: Flagellin FljN
V: Flagellin FljN
W: Flagellin FljN
X: Flagellin FljN
Y: Flagellin FljN
Z: Flagellin FljN
a: Flagellin FljN
b: Flagellin FljN
c: Flagellin FljN
d: Flagellin FljN
e: Flagellin FljN
f: Flagellin FljN
g: Flagellin FljN
h: Flagellin FljN
i: Flagellin FljN
j: Flagellin FljN
k: Flagellin FljN
l: Flagellin FljN
m: Flagellin FljN
n: Flagellin FljN
o: Flagellin FljN
p: Flagellin FljN
q: Flagellin FljN
r: Flagellin FljN


Theoretical massNumber of molelcules
Total (without water)1,229,76744
Polymers1,229,76744
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin FljN


Mass: 27949.256 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides (bacteria) / Strain: NA1000 / References: UniProt: O52530

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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: FljN flagellar filament (symmetrized) / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.28 kDa/nm / Experimental value: NO
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 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 FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 70 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
13cryoSPARC4.43D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.923 ° / Axial rise/subunit: 4.778 Å / Axial symmetry: C1
3D reconstructionResolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131070 / Symmetry type: HELICAL
Atomic model buildingB value: 67 / Space: REAL
Atomic model buildingAccession code: AF-O52530-F1 / Source name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00885668
ELECTRON MICROSCOPYf_angle_d0.686115984
ELECTRON MICROSCOPYf_dihedral_angle_d4.28512012
ELECTRON MICROSCOPYf_chiral_restr0.0514960
ELECTRON MICROSCOPYf_plane_restr0.00514828

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