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- EMDB-52465: CryoEM structure of Asgard AtubA/B microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-52465
TitleCryoEM structure of Asgard AtubA/B microtubule
Map data
Sample
  • Complex: microtubule structure of Asgard tubulins AtubA/B
    • Protein or peptide: Asgard tubulin AtubA
    • Protein or peptide: Asgard tubulin AtubB
KeywordsAsgard archaea / microtubule / cryoEM / cytomotive filaments / cytoskeleton / STRUCTURAL PROTEIN
Biological speciesCandidatus Lokiarchaeum ossiferum (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWollweber F / Xu J / Ponce-Toledo RI / Rodrigues-Oliveira T / Malit JJL / Kokhanovska A / Wieczorek M / Schleper C / Pilhofer M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101000232European Union
CitationJournal: Cell / Year: 2025
Title: Microtubules in Asgard archaea.
Authors: Florian Wollweber / Jingwei Xu / Rafael I Ponce-Toledo / Florina Marxer / Thiago Rodrigues-Oliveira / Anja Pössnecker / Zhen-Hao Luo / Jessie James Limlingan Malit / Anastasiia Kokhanovska ...Authors: Florian Wollweber / Jingwei Xu / Rafael I Ponce-Toledo / Florina Marxer / Thiago Rodrigues-Oliveira / Anja Pössnecker / Zhen-Hao Luo / Jessie James Limlingan Malit / Anastasiia Kokhanovska / Michal Wieczorek / Christa Schleper / Martin Pilhofer /
Abstract: Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling ...Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling into microtubules remains unclear. Here, we report the discovery of microtubule-forming tubulins in Asgard archaea, the closest known relatives of eukaryotes. These Asgard tubulins (AtubA/B) are closely related to eukaryotic α/β-tubulins and the enigmatic bacterial tubulins BtubA/B. Proteomics of Candidatus Lokiarchaeum ossiferum showed that AtubA/B were highly expressed. Cryoelectron microscopy structures demonstrate that AtubA/B form eukaryote-like heterodimers, which assembled into 5-protofilament bona fide microtubules in vitro. The additional paralog AtubB2 lacks a nucleotide-binding site and competitively displaced AtubB. These AtubA/B2 heterodimers polymerized into 7-protofilament non-canonical microtubules. In a sub-population of Ca. Lokiarchaeum ossiferum cells, cryo-tomography revealed tubular structures, while expansion microscopy identified AtubA/B cytoskeletal assemblies. Our findings suggest a pre-eukaryotic origin of microtubules and provide a framework for understanding the fundamental principles of microtubule assembly.
History
DepositionJan 7, 2025-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52465.png

Downloads & links

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Map

FileDownload / File: emd_52465.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 383.4 Å		1.07 Å/pix.
x 360 pix.
= 383.4 Å		1.07 Å/pix.
x 360 pix.
= 383.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.055970106 - 0.075423464
Average (Standard dev.)0.000038381953 (±0.003354792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52465_msk_1.map
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Half map: #1

Fileemd_52465_half_map_1.map
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Half map: #2

Fileemd_52465_half_map_2.map
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Sample components

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Entire : microtubule structure of Asgard tubulins AtubA/B

EntireName: microtubule structure of Asgard tubulins AtubA/B
Components
  • Complex: microtubule structure of Asgard tubulins AtubA/B
    • Protein or peptide: Asgard tubulin AtubA
    • Protein or peptide: Asgard tubulin AtubB

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Supramolecule #1: microtubule structure of Asgard tubulins AtubA/B

SupramoleculeName: microtubule structure of Asgard tubulins AtubA/B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)

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Macromolecule #1: Asgard tubulin AtubA

MacromoleculeName: Asgard tubulin AtubA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGEIVCIQV GQAGNQIAGA FWQKICAEHG IDPVNGKAID VVGDTDIFFN TIGDKYIPRA VVVDLEPAV VENIREKFGT LFDPKSIVSG ADGAGNNFAI GFNEHGAETL EKVMQVVEQR V SETESIGG FILTHSCGGG TGSGFGSKIL KTIRERYPKV PIFTFSIFPS ...String:
MAGEIVCIQV GQAGNQIAGA FWQKICAEHG IDPVNGKAID VVGDTDIFFN TIGDKYIPRA VVVDLEPAV VENIREKFGT LFDPKSIVSG ADGAGNNFAI GFNEHGAETL EKVMQVVEQR V SETESIGG FILTHSCGGG TGSGFGSKIL KTIRERYPKV PIFTFSIFPS PKISETVVEP YN AIMTLSN LIKYASCSIV LDNEALFSIA EKKLEVENPS LEDLNLIIAQ VLTNVTASLR FSG TLNLDL GKLVTNLVPF SNLHFLMAST APLVLAGKES YEKMTAKELS AQVFGDEYIC AACK PTTGR YLAASVLFRG AVKTSDVNEA MATVKEQNSF VNWIPTGFKI SKSETSPKDS ALGVI MLGN NSEIVSVFER IGANFDRLWS RKAFAHWFTD SGFEEKDLDD ARALVQKVID DYRKLT EDA

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Macromolecule #2: Asgard tubulin AtubB

MacromoleculeName: Asgard tubulin AtubB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeum ossiferum (archaea)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGREVIMLHV GQAGIQVGAM YWKQICAEHN LDHNGAPIGG DIKGDPDCFF MKASGGKYVP RALLIDLEP KVVRQVGNEQ LPSFFDPKNL IHGLYGGANS FAKGYLGEGR DMIDNIMEQL K KEVAKCES LQGFIMTHAV GGGSGGGLGC LIMEKIKEEY PKKILWSYSI ...String:
MGREVIMLHV GQAGIQVGAM YWKQICAEHN LDHNGAPIGG DIKGDPDCFF MKASGGKYVP RALLIDLEP KVVRQVGNEQ LPSFFDPKNL IHGLYGGANS FAKGYLGEGR DMIDNIMEQL K KEVAKCES LQGFIMTHAV GGGSGGGLGC LIMEKIKEEY PKKILWSYSI LPSPLLSDAV VE PYNAILS LDKMIQYTDE TVVIDNHALF QIVTKNMGID DPIYDDLNHV ISQALSDITA SLR FKGSLN TDMKEFLVNL VPYPRSHFLM ASFAPMATAE DRQYAKLTTS NLANALFEEN YMMA AVDVT KGTFLACSLL FRGENTAQDI TNALLDIKGR IKFSSFIPTG IKYGMTGTAP EGLER SGSA LINHTGVAEI FNRILAQFNL MFDKGAFLNW YEIEGMSKDD FAGARDNVQK LSDEYK RDE E

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
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: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Details: the initial model is generated from sub-tomogram average.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130437
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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