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- PDB-9sj2: Calcium coordinated ABPX fibers from Pyrodictium abyssi -

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Basic information

Entry
Database: PDB / ID: 9sj2
TitleCalcium coordinated ABPX fibers from Pyrodictium abyssi
ComponentsAbpX
KeywordsSTRUCTURAL PROTEIN / Fiber / Helical / Filament / Hyperthermophile / Calcium binding / Donor strand complementation / Pyrodictium abyssi / Extracellular matrix / Biomatrix / Sinusoidal filament
Biological speciesPyrodictium abyssi DSM 6158 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsSleutel, M. / Sogues, A. / Remaut, H. / Conticello, V. / Socorro, A.
Funding support Belgium, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: AbpX
D: AbpX
E: AbpX
B: AbpX
A: AbpX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,06220
Polymers87,4615
Non-polymers60115
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
AbpX


Mass: 17492.217 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrodictium abyssi DSM 6158 (archaea) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Helical assembly of AbpX protomers / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Pyrodictium abyssi DSM 6158 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -53.971 ° / Axial rise/subunit: 44.013 Å / Axial symmetry: C1
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1572118 / Symmetry type: HELICAL
RefinementHighest resolution: 3.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036140
ELECTRON MICROSCOPYf_angle_d0.588402
ELECTRON MICROSCOPYf_dihedral_angle_d4.799826
ELECTRON MICROSCOPYf_chiral_restr0.0431058
ELECTRON MICROSCOPYf_plane_restr0.0031103

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