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- EMDB-18700: Sulfolobus acidocaldarius Archaellum filament. -

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Basic information

Entry
Database: EMDB / ID: EMD-18700
TitleSulfolobus acidocaldarius Archaellum filament.
Map data
Sample
  • Organelle or cellular component: Filament
    • Protein or peptide: Flagellin
Keywordscell surface appendage / N-glycosylation / PROTEIN FIBRIL
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellin
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsIsupov MN / Gaines M / McLaren M / Daum B
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: To Be Published
Title: Sulfolobus acidocaldarius Archaellum filament.
Authors: Isupov MN / Gaines M / McLaren M / Daum B
History
DepositionOct 22, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18700.png

Downloads & links

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Map

FileDownload / File: emd_18700.map.gz / Format: CCP4 / Size: 91.1 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 288 pix.
= 238.752 Å		0.83 Å/pix.
x 288 pix.
= 238.752 Å		0.83 Å/pix.
x 288 pix.
= 238.752 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.829 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.043653537 - 0.16486481
Average (Standard dev.)0.003694864 (±0.0126816705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 238.752 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18700_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18700_half_map_2.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 : Filament

EntireName: Filament
Components
  • Organelle or cellular component: Filament
    • Protein or peptide: Flagellin

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Supramolecule #1: Filament

SupramoleculeName: Filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus acidocaldarius (acidophilic)
Molecular weightTheoretical: 31.209258 KDa
SequenceString: LAGLDTAIIL IAFIITAAVL AYVAVNMGLF VTQKAKTTIN KGEETASTAL SLSGNVLYAV NYPTNTKSYW MYFTVSPSSG VSSVDLSPS TTAISFTAAS RGVSLSNIYQ FSLLSVLPSQ VNNKVQVKLG TSIINLTLAF SSNSAGQTYV YYSDPNYALL A LNYTLGQE ...String:
LAGLDTAIIL IAFIITAAVL AYVAVNMGLF VTQKAKTTIN KGEETASTAL SLSGNVLYAV NYPTNTKSYW MYFTVSPSSG VSSVDLSPS TTAISFTAAS RGVSLSNIYQ FSLLSVLPSQ VNNKVQVKLG TSIINLTLAF SSNSAGQTYV YYSDPNYALL A LNYTLGQE VKGGQLTSSP LYIISNTSIV ASKPWLKNDN VFTFNISVNG TEVEYYAYVN KTFAFTYPVS GFPLAGSDIA PA GSVIGVM ILFGPGEATN VFQYETVTIQ ITPNIGSPLT ISQYIYQPDG KVTVIG

UniProtKB: Flagellin

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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: 3
VitrificationCryogen name: ETHANE
DetailsMixed population of filaments isolated from Sulfolobus acidocaldarius

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 3 / Number real images: 20579 / Average exposure time: 2.57 sec. / Average electron dose: 43.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.433 Å
Applied symmetry - Helical parameters - Δ&Phi: 107.947 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 1059736
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsJligand was used for preparing dictionaries for an unusual sugars
RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL
Output model

PDB-8qx4:
Sulfolobus acidocaldarius Archaellum filament.

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