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- EMDB-54935: Calcium coordinated ABPX fibers from Pyrodictium abyssi -

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Basic information

Entry
Database: EMDB / ID: EMD-54935
TitleCalcium coordinated ABPX fibers from Pyrodictium abyssi
Map dataSharpened with B-factor -50
Sample
  • Complex: Helical assembly of AbpX protomers
    • Protein or peptide: AbpX
  • Ligand: CALCIUM ION
KeywordsFiber / Helical / Filament / Hyperthermophile / Calcium binding / Donor strand complementation / Pyrodictium abyssi / Extracellular matrix / Biomatrix / Sinusoidal filament / STRUCTURAL PROTEIN
Biological speciesPyrodictium abyssi DSM 6158 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsSleutel M / Sogues A / Remaut H / Conticello V / Socorro A
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: To Be Published
Title: Calcium coordinated ABPX fibers from Pyrodictium abyssi
Authors: Sleutel M / Sogues A / Remaut H / Conticello V / Socorro A
History
DepositionAug 29, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54935.png

Downloads & links

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Map

FileDownload / File: emd_54935.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened with B-factor -50
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 400 pix.
= 278. Å		0.7 Å/pix.
x 400 pix.
= 278. Å		0.7 Å/pix.
x 400 pix.
= 278. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.695 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.067162484 - 0.13656518
Average (Standard dev.)0.000058518603 (±0.002491889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 278.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54935_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Post-processed with EMReady

Fileemd_54935_additional_1.map
AnnotationPost-processed with EMReady
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54935_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_54935_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 : Helical assembly of AbpX protomers

EntireName: Helical assembly of AbpX protomers
Components
  • Complex: Helical assembly of AbpX protomers
    • Protein or peptide: AbpX
  • Ligand: CALCIUM ION

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Supramolecule #1: Helical assembly of AbpX protomers

SupramoleculeName: Helical assembly of AbpX protomers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrodictium abyssi DSM 6158 (archaea)

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Macromolecule #1: AbpX

MacromoleculeName: AbpX / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pyrodictium abyssi DSM 6158 (archaea)
Molecular weightTheoretical: 17.492217 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QWSETLSLSA TISTGSLDVD IKANEATDVT TSSQYIDVSL SLTSTDSDQG NEQLSITIEK AYPGAEVNVT FTLENVGTIP ALATIKLNT DTIPSDVAAC VNVKLYNAQG NPINTPYTIQ LAPGEFEKFK LGIEIPSSCD LEENKKDAIQ LNNIVEVDVE Q NVS

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 15 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 1.2 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 44.013 Å
Applied symmetry - Helical parameters - Δ&Phi: -53.971 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1572118
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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