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- EMDB-44404: Cryo-EM of Hyper2 tube, ~24 nm diameter -

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Basic information

Entry
Database: EMDB / ID: EMD-44404
TitleCryo-EM of Hyper2 tube, ~24 nm diameter
Map data
Sample
  • Complex: Hyper2 tube
    • Protein or peptide: DUF1102 domain-containing protein
  • Ligand: CALCIUM ION
KeywordsHyper2 / Protein tube / Helical tube / Strand donation / PROTEIN FIBRIL
Function / homologyDUF1102 domain-containing protein
Function and homology information
Biological speciesHyperthermus sp. (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSonani RR / Miller JG / Conticello V / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122150 United States
CitationJournal: Nat Commun / Year: 2025
Title: Donor strand complementation and calcium ion coordination drive the chaperone-free polymerization of archaeal cannulae.
Authors: Mike Sleutel / Ravi R Sonani / Jessalyn G Miller / Fengbin Wang / Andres Gonzalez Socorro / Yang Chen / Reece Martin / Borries Demeler / Michael J Rudolph / Vikram Alva / Han Remaut / Edward ...Authors: Mike Sleutel / Ravi R Sonani / Jessalyn G Miller / Fengbin Wang / Andres Gonzalez Socorro / Yang Chen / Reece Martin / Borries Demeler / Michael J Rudolph / Vikram Alva / Han Remaut / Edward H Egelman / Vincent P Conticello /
Abstract: Cannulae are structurally rigid tubular protein filaments that accumulate on the extracellular surface of archaea within the family Pyrodictiaceae during cell growth. These obligate anaerobes ...Cannulae are structurally rigid tubular protein filaments that accumulate on the extracellular surface of archaea within the family Pyrodictiaceae during cell growth. These obligate anaerobes propagate under hyperthermophilic conditions in which cannulae form a biomatrix that interconnects and sustains cells. The persistence of cannulae in this environment suggests that these filaments display significant thermostability, which has attracted technological interest in their development as synthetic protein-based biomaterials. Here, we report cryoEM structural analyses of ex vivo and in vitro assembled recombinant cannulae. We demonstrate that the interactions between protomers in native and recombinant cannulae is based on donor strand complementation (DSC), a form of non-covalent polymerization previously observed for bacterial chaperone-usher pili. Unexpectedly, calcium ion coordination at the subunit interfaces reinforces the network of donor strand interactions in the cannulae. This study provides insight into the mechanism of assembly of cannulae and the structural origin of their high stability and rigidity.
History
DepositionApr 3, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44404.png

Downloads & links

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Map

FileDownload / File: emd_44404.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.07732865 - 0.13637877
Average (Standard dev.)0.00015725946 (±0.009133912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened Map

Fileemd_44404_additional_1.map
AnnotationSharpened Map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_44404_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_44404_half_map_2.map
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Sample components

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Entire : Hyper2 tube

EntireName: Hyper2 tube
Components
  • Complex: Hyper2 tube
    • Protein or peptide: DUF1102 domain-containing protein
  • Ligand: CALCIUM ION

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Supramolecule #1: Hyper2 tube

SupramoleculeName: Hyper2 tube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Hyperthermus sp. (archaea)

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Macromolecule #1: DUF1102 domain-containing protein

MacromoleculeName: DUF1102 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hyperthermus sp. (archaea)
Molecular weightTheoretical: 16.234279 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSVTSDRTYY GYGDVSVKNE PVNVVVSPFS FPGANASLSS GGQGVFKKPD WIRVVNQSDV ENVKLEIDWV NANQAANYFD YARILVTGP NGQVKGYLSL QHGKAWITLD AEELREGAVL GAVMYYEVKE GVLASRLPLV FKVRVVETG

UniProtKB: DUF1102 domain-containing protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.424 Å
Applied symmetry - Helical parameters - Δ&Phi: 46.23 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95418
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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