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- PDB-9bac: Cryo-EM of Hyper2 tube, ~24 nm diameter -

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Basic information

Entry
Database: PDB / ID: 9bac
TitleCryo-EM of Hyper2 tube, ~24 nm diameter
ComponentsDUF1102 domain-containing protein
KeywordsPROTEIN FIBRIL / Hyper2 / Protein tube / Helical tube / Strand donation
Function / homologyDUF1102 domain-containing protein
Function and homology information
Biological speciesHyperthermus sp. (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSonani, R.R. / Miller, J.G. / Conticello, V. / Egelman, E.H.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
z: DUF1102 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3554
Polymers16,2341
Non-polymers1203
Water00
1
z: DUF1102 domain-containing protein
hetero molecules
x 66


Theoretical massNumber of molelcules
Total (without water)1,079,398264
Polymers1,071,46266
Non-polymers7,935198
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
helical symmetry operation65
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 66 / Rise per n subunits: 1.424 Å / Rotation per n subunits: 46.23 °)

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Components

#1: Protein DUF1102 domain-containing protein / Hyper2


Mass: 16234.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyperthermus sp. (archaea) / Gene: DSY37_03180 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A432R7L7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Hyper2 tube / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Hyperthermus sp. (archaea)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.15.2_3472: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 46.23 ° / Axial rise/subunit: 1.424 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95418 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0081164
ELECTRON MICROSCOPYf_angle_d0.7831585
ELECTRON MICROSCOPYf_dihedral_angle_d20.223681
ELECTRON MICROSCOPYf_chiral_restr0.057176
ELECTRON MICROSCOPYf_plane_restr0.005206

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