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- EMDB-45504: Caulobacter crescentus FljJL flagellar filament (asymmetrical) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-45504
TitleCaulobacter crescentus FljJL flagellar filament (asymmetrical)
Map data
Sample
  • Complex: FljJL flagellar filament (asymmetrical)
    • Protein or peptide: Flagellin FljL
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 FljL
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 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_45504.png

Downloads & links

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Map

FileDownload / File: emd_45504.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: 0.38
Minimum - Maximum-1.5552784 - 2.7128103
Average (Standard dev.)0.0029853522 (±0.10574585)
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_45504_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 : FljJL flagellar filament (asymmetrical)

EntireName: FljJL flagellar filament (asymmetrical)
Components
  • Complex: FljJL flagellar filament (asymmetrical)
    • Protein or peptide: Flagellin FljL

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Supramolecule #1: FljJL flagellar filament (asymmetrical)

SupramoleculeName: FljJL flagellar filament (asymmetrical) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000

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Macromolecule #1: Flagellin FljL

MacromoleculeName: Flagellin FljL / type: protein_or_peptide / ID: 1 / Number of copies: 37 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter vibrioides (bacteria) / Strain: NA1000
Molecular weightTheoretical: 28.260658 KDa
SequenceString: MLNSINTNPG ALLALQNLNS TNTELAATQG RINTGKKVAN AKDNGAIWSM AKMQSATASS LNSVKDSLQR GQSTIDVALA AGDTITDLL TKMKEKALAA SDTSLNTASF NALKADFESL RDQLQKAATN AKFNGVSLAD GSTTKLSFLA NEDGSNFTVT A QTLSLTGI ...String:
MLNSINTNPG ALLALQNLNS TNTELAATQG RINTGKKVAN AKDNGAIWSM AKMQSATASS LNSVKDSLQR GQSTIDVALA AGDTITDLL TKMKEKALAA SDTSLNTASF NALKADFESL RDQLQKAATN AKFNGVSLAD GSTTKLSFLA NEDGSNFTVT A QTLSLTGI GLTATSTFTD AATAKTMIAT ITTSLQTATN KLSSLGTSSV GLDTHLTFVG KLQDSLDAGV GNLVDADLAK ES AKLQSLQ TKQQLGVQAL SIANQTPQTI LSLFKG

UniProtKB: Flagellin FljL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle 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

Startup modelType of model: OTHER / Details: Featureless Cylinder
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 436137
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9cem:
Caulobacter crescentus FljJL flagellar filament (asymmetrical)

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