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- PDB-9tqj: Cryo-EM structure of AtubAB heterodimer from Heimdallarchaeia -

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Basic information

Entry
Database: PDB / ID: 9tqj
TitleCryo-EM structure of AtubAB heterodimer from Heimdallarchaeia
Components
  • AtubA
  • AtubB
KeywordsUNKNOWN FUNCTION / Microtubules / BtubAB / cytoskeleton / asgard archaea / eukaryogenesis
Function / homologyGUANOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesCandidatus Heimdallarchaeota archaeon (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLowe, J. / von Kugelgen, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
Wellcome Trust203276/C/16/Z United Kingdom
Wellcome Trust227876/Z/23/Z United Kingdom
Wellcome Trust227452/Z/23/Z United Kingdom
CitationJournal: To Be Published
Title: Asgard archaeal AtubAB tubulins form mini microtubules exhibiting dynamic instability
Authors: Lowe, J. / von Kugelgen, A.
History
DepositionDec 22, 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: 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
A: AtubA
B: AtubB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9983
Polymers94,5552
Non-polymers4431
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 AtubA


Mass: 48279.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon (archaea)
Plasmid: pHis17-AtubAB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Protein AtubB


Mass: 46275.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon (archaea)
Plasmid: pHis17-AtubAB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AtubAB heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 94 kDa/nm / Experimental value: YES
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pHis17-AtubAB
Buffer solutionpH: 7.7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen 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: 2500 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
12RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125647 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076133
ELECTRON MICROSCOPYf_angle_d1.1448314
ELECTRON MICROSCOPYf_dihedral_angle_d5.037830
ELECTRON MICROSCOPYf_chiral_restr0.043951
ELECTRON MICROSCOPYf_plane_restr0.0041068

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