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- PDB-8uxn: Caulobacter crescentus FljM flagellar filament (symmetrized) -

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Basic information

Entry
Database: PDB / ID: 8uxn
TitleCaulobacter crescentus FljM flagellar filament (symmetrized)
ComponentsFlagellin FljM
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 FljM
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.11 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
DepositionNov 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 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 FljM
B: Flagellin FljM
C: Flagellin FljM
D: Flagellin FljM
E: Flagellin FljM
F: Flagellin FljM
G: Flagellin FljM
H: Flagellin FljM
I: Flagellin FljM
J: Flagellin FljM
K: Flagellin FljM
L: Flagellin FljM
M: Flagellin FljM
N: Flagellin FljM
O: Flagellin FljM
P: Flagellin FljM
Q: Flagellin FljM
R: Flagellin FljM
S: Flagellin FljM
T: Flagellin FljM
U: Flagellin FljM
V: Flagellin FljM
W: Flagellin FljM
X: Flagellin FljM
Y: Flagellin FljM
Z: Flagellin FljM
a: Flagellin FljM
b: Flagellin FljM
c: Flagellin FljM
d: Flagellin FljM
e: Flagellin FljM
f: Flagellin FljM
g: Flagellin FljM
h: Flagellin FljM
i: Flagellin FljM
j: Flagellin FljM
k: Flagellin FljM
l: Flagellin FljM
m: Flagellin FljM
n: Flagellin FljM
o: Flagellin FljM
p: Flagellin FljM
q: Flagellin FljM
r: Flagellin FljM


Theoretical massNumber of molelcules
Total (without water)1,229,81144
Polymers1,229,81144
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin FljM


Mass: 27950.240 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Source: (natural) Caulobacter vibrioides (bacteria) / Strain: NA1000 / References: UniProt: O52529

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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: FljM 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
Buffer componentName: phosphate buffered saline
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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: 45 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

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1Topazparticle selectiontopaz-filament
2EPUimage acquisition
4RELION4CTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10RELION4initial Euler assignment
11cryoSPARC4.1final Euler assignment
12cryoSPARC4.1classification
13cryoSPARC4.13D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.93 ° / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
3D reconstructionResolution: 2.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 248115 / Symmetry type: HELICAL
Atomic model buildingB value: 67 / Space: REAL
Atomic model buildingAccession code: O52529 / Source name: AlphaFold
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00885448
ELECTRON MICROSCOPYf_angle_d0.665115632
ELECTRON MICROSCOPYf_dihedral_angle_d4.46611968
ELECTRON MICROSCOPYf_chiral_restr0.04814872
ELECTRON MICROSCOPYf_plane_restr0.00414784

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