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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: Proc Natl Acad Sci U S A / Year: 2026
Title: AbpX reveals a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels.
Authors: Mike Sleutel / Adrià Sogues / Andres Gonzalez Socorro / Vita Cooman / Marcus Fislage / Adam K Nijhawan / Xiaobing Zuo / Vikram Alva / Han Remaut / Vincent P Conticello /
Abstract: Evolutionary pressure on microbial communities propagating under extreme environmental conditions often results in unique structural adaptations to promote cell survival. Here, we report an ...Evolutionary pressure on microbial communities propagating under extreme environmental conditions often results in unique structural adaptations to promote cell survival. Here, we report an investigation of AbpX, a biomatrix protein identified in cultures of the hyperthermophilic archaeon . Under ex vivo and in vitro conditions, AbpX assembles into a paracrystalline lattice composed of semiflexible fibrils. CryoEM analysis of recombinant AbpX fibrils reveals that the precursor protein polymerizes through donor strand complementation (DSC), a process previously reported for chaperone-usher fimbriae in Gram-negative bacteria. Unlike the latter DSC protein polymers, AbpX undergoes chaperone-free polymerization in the presence of calcium ions, which are sequestered at the donor strand-acceptor groove interface between protomers in the fibril. Using a combination of cryoEM and crystallographic information, a structural model is proposed for the AbpX lattice that provides insight into its potential role in biofilm formation. These findings suggest that calcium ion coordination may contribute to fibril assembly and preorganize fibrils for incorporation into the protein lattice. Bioinformatic analysis indicates that AbpX exemplifies a distinct and broadly distributed clade of calcium ion responsive biomatrix proteins within the TasA superfamily that can be fabricated into hydrogel biomaterials in vitro under environmentally benign conditions.
History
DepositionAug 29, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 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

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.695 Å
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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
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Additional map: Post-processed with EMReady

Fileemd_54935_additional_1.map
AnnotationPost-processed with EMReady
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Half map: #2

Fileemd_54935_half_map_1.map
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Half map: #1

Fileemd_54935_half_map_2.map
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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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