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- EMDB-45500: Caulobacter crescentus FljN flagellar filament (symmetrized) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-45500
TitleCaulobacter crescentus FljN flagellar filament (symmetrized)
Map data
Sample
  • Complex: FljN flagellar filament (symmetrized)
    • Protein or peptide: Flagellin FljN
Keywordsflagellin / flagellar filament / STRUCTURAL PROTEIN
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.22 Å
AuthorsSanchez JC / Montemayor EJ / Ploscariu NT / Parrell D / Baumgardt JK / Yang JE / Sibert B / Cai K / Wright ER
Funding support United States, 5 items
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 JC / Montemayor EJ / Ploscariu NT / Parrell D / Baumgardt JK / Yang JE / Sibert B / Cai K / Wright ER
History
DepositionJun 26, 2024-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateAug 28, 2024-
Current statusAug 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45500.png

Downloads & links

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Map

FileDownload / File: emd_45500.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 427.008 Å		0.83 Å/pix.
x 512 pix.
= 427.008 Å		0.83 Å/pix.
x 512 pix.
= 427.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.512
Minimum - Maximum-1.4295454 - 2.897621
Average (Standard dev.)0.007063868 (±0.1306177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 427.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45500_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FljN flagellar filament (symmetrized)

EntireName: FljN flagellar filament (symmetrized)
Components
  • Complex: FljN flagellar filament (symmetrized)
    • Protein or peptide: Flagellin FljN

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Supramolecule #1: FljN flagellar filament (symmetrized)

SupramoleculeName: FljN flagellar filament (symmetrized) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000
Molecular weightTheoretical: 0.28 kDa/nm

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Macromolecule #1: Flagellin FljN

MacromoleculeName: Flagellin FljN / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000
Molecular weightTheoretical: 27.949256 KDa
SequenceString: MALNSINTNS GALIALQNLN STNAELTQVQ QRINTGKKIG SAKDNGAIWA TAKNQSATAN SMNAVKDSLQ RGQSTIDVAL AAGDTITDL LGKMKEKALA ASDTSLNTAS FNALKSDFDS LRDQITKAAS NAKFNGVSIA NGSTAKLTFL ANSDGSGFTV T AKTLTLTG ...String:
MALNSINTNS GALIALQNLN STNAELTQVQ QRINTGKKIG SAKDNGAIWA TAKNQSATAN SMNAVKDSLQ RGQSTIDVAL AAGDTITDL LGKMKEKALA ASDTSLNTAS FNALKSDFDS LRDQITKAAS NAKFNGVSIA NGSTAKLTFL ANSDGSGFTV T AKTLTLTG LGLTASSTFT TAAAAKTMIG TIDTALQTAT NKLASLGTSS TGLDTHLTFV GKLQDSLDAG VGNLVDADLA KE SAKLQSL QTKQQLGVQA LSIANSSSSA ILSLFR

UniProtKB: Flagellin FljN

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.778 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.923 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 131070
Startup modelType of model: OTHER / Details: Featureless Cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

0-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Overall B value: 67
Output model

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

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