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- EMDB-19168: Oxiplasma meridianum archaellum -

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Basic information

Entry
Database: EMDB / ID: EMD-19168
TitleOxiplasma meridianum archaellum
Map data
Sample
  • Organelle or cellular component: Oxiplasma meridianum archaellum
    • Protein or peptide: Oxiplasma meridianum archaellum
  • Ligand: beta-D-galactopyranose
Keywordscell surface appendage / N-glycosylation / PROTEIN FIBRIL
Biological speciesOxyplasma meridianum (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsIsupov MN / Gaines M / Daum B / McLaren M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)109784European Union
CitationJournal: To Be Published
Title: CryoEM of Oxiplasma meridianum archaellum
Authors: Isupov MN / Gaines M / Daum B / Hanus C
History
DepositionDec 14, 2023-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19168.png

Downloads & links

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Map

FileDownload / File: emd_19168.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.043801133 - 0.16378058
Average (Standard dev.)0.0013867731 (±0.010521071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19168_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_19168_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 : Oxiplasma meridianum archaellum

EntireName: Oxiplasma meridianum archaellum
Components
  • Organelle or cellular component: Oxiplasma meridianum archaellum
    • Protein or peptide: Oxiplasma meridianum archaellum
  • Ligand: beta-D-galactopyranose

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Supramolecule #1: Oxiplasma meridianum archaellum

SupramoleculeName: Oxiplasma meridianum archaellum / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oxyplasma meridianum (archaea)

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Macromolecule #1: Oxiplasma meridianum archaellum

MacromoleculeName: Oxiplasma meridianum archaellum / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Oxyplasma meridianum (archaea)
Molecular weightTheoretical: 23.887668 KDa
SequenceString: ETGIGTLIIF IAMVLVAAVA ATVLINTAGS LQQRATSTGS QTTNQVSTGL IVQSIYGMDN NRSNPESGSL NWTAIYVTLN TGSSPVDLS NVSLSLEYQG QLASLKYTPA TTNASFAVDT NGTSNVFSVL NAGVGYKNST ATFKNVELKN VTKSTNFAIV V IRDPSNSL ...String:
ETGIGTLIIF IAMVLVAAVA ATVLINTAGS LQQRATSTGS QTTNQVSTGL IVQSIYGMDN NRSNPESGSL NWTAIYVTLN TGSSPVDLS NVSLSLEYQG QLASLKYTPA TTNASFAVDT NGTSNVFSVL NAGVGYKNST ATFKNVELKN VTKSTNFAIV V IRDPSNSL TSSHPVLTTG SEVVILVNTS AVFGGMKQGQ AVTGQINPSV GSPGIIQFTT PSAFTETVME LQ

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Macromolecule #5: beta-D-galactopyranose

MacromoleculeName: beta-D-galactopyranose / type: ligand / ID: 5 / Number of copies: 64 / Formula: GAL
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GAL:
beta-D-galactopyranose

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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: 1
VitrificationCryogen name: ETHANE
DetailsOxiplasma meridianum archaellum

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.45 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.641 Å
Applied symmetry - Helical parameters - Δ&Phi: 107.922 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1374113
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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