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- EMDB-69786: Heimdallarchaeales alpha/beta tubulin microtubule with a single seam -

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Basic information

Entry
Database: EMDB / ID: EMD-69786
TitleHeimdallarchaeales alpha/beta tubulin microtubule with a single seam
Map dataHeim-alpha/beta-tubulin microtubule with single seam
Sample
  • Complex: Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
    • Protein or peptide: Heim-alpha-tubulin
    • Protein or peptide: Heim-beta-tubulin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHeimdallarchaea / tubulin / microtubule / archaea / PROTEIN FIBRIL
Biological speciesCandidatus Heimdallarchaeaceae (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTran LT / Ali S / Matsumoto T / Yamazaki Y / Narita A / Miyazaki M / Robinson RC
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25K18436 Japan
Japan Society for the Promotion of Science (JSPS)22H05171 Japan
Japan Society for the Promotion of Science (JSPS)23764079 Japan
Other private2025-4021 Japan
Other private Japan
Other private500230057 Japan
Japan Science and TechnologyJPMJFR2417 Japan
Other private Japan
CitationJournal: To Be Published
Title: Structure and dynamics of a four-protofilament microtubule from Heimdallarchaeales alpha/beta-tubulin
Authors: Tran LT / Ali S / Matsumoto T / Yamazaki Y / Narita A / Miyazaki M / Robinson RC
History
DepositionMar 18, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69786.png

Downloads & links

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Map

FileDownload / File: emd_69786.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHeim-alpha/beta-tubulin microtubule with single seam
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 301.176 Å		0.75 Å/pix.
x 400 pix.
= 301.176 Å		0.75 Å/pix.
x 400 pix.
= 301.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.009708242 - 0.021169186
Average (Standard dev.)0.00012766384 (±0.0010071265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 301.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2 of Heim-alpha/beta-tubulin microtubule with single seam

Fileemd_69786_half_map_1.map
AnnotationHalf map 2 of Heim-alpha/beta-tubulin microtubule with single seam
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of Heim-alpha/beta-tubulin microtubule with single seam

Fileemd_69786_half_map_2.map
AnnotationHalf map 1 of Heim-alpha/beta-tubulin microtubule with single seam
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heimdallarchaeales alpha/beta tubulin microtubule with a single seam

EntireName: Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
Components
  • Complex: Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
    • Protein or peptide: Heim-alpha-tubulin
    • Protein or peptide: Heim-beta-tubulin
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Heimdallarchaeales alpha/beta tubulin microtubule with a single seam

SupramoleculeName: Heimdallarchaeales alpha/beta tubulin microtubule with a single seam
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Candidatus Heimdallarchaeaceae (archaea)

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Macromolecule #1: Heim-alpha-tubulin

MacromoleculeName: Heim-alpha-tubulin / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeaceae (archaea)
Molecular weightTheoretical: 46.27507 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSREIISIHV GQAGLQVGAA FWRTVLEEHG LGNDGSVVDA SKEKSAVYFK QAGNNKFVPR AILVDLEPMV IKTIMNDLPG LFDPAYTIH GQSGAANNWA RGYRGADGEV NVDDVLKIVE KAVSETDSLQ GFSISHSIGG GTGSGLGSQI LKKLKETYPK Y PIITFSVF ...String:
MSREIISIHV GQAGLQVGAA FWRTVLEEHG LGNDGSVVDA SKEKSAVYFK QAGNNKFVPR AILVDLEPMV IKTIMNDLPG LFDPAYTIH GQSGAANNWA RGYRGADGEV NVDDVLKIVE KAVSETDSLQ GFSISHSIGG GTGSGLGSQI LKKLKETYPK Y PIITFSVF PSPLISDAVT EPYNSVFALD HLIEYADETI VLDNHALYNL TKNNMGIKSP SYADLNKIIS WVMSGVTASL RF KGDLNTD LKELLVNLVP FPRQHFLTST FSPIKNGTGS FEEVTTHDII NQLFDPNNAM SDTNFDEGAY IASVVMMRGH EVK TNAVNS SLAEIKGKLR FSEFIPTGIK TGVTSETLVG FESTGLNLSN HTGITKVFKR LAAQFDAMYE RDAFVHWYLG EGMS KDDME KARENLGKLT TEYDTSV

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Macromolecule #2: Heim-beta-tubulin

MacromoleculeName: Heim-beta-tubulin / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeaceae (archaea)
Molecular weightTheoretical: 48.320492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGEVVVVAV GQAGNQIADQ FWQLIAQEHK IGLDGMPTNG EPTGRTDVFF RKVSNRYVPR AVLVDLEPAV LKSVSDDAKP NFYDPKNKV HGADGAGNNF AVGHTEMGAQ YLEQVIGKIK NEVEKTDSLG GFIVTHSVGG GTGSGFGTLI MQNIRKEYPN T PLLSFSIY ...String:
MAGEVVVVAV GQAGNQIADQ FWQLIAQEHK IGLDGMPTNG EPTGRTDVFF RKVSNRYVPR AVLVDLEPAV LKSVSDDAKP NFYDPKNKV HGADGAGNNF AVGHTEMGAQ YLEQVIGKIK NEVEKTDSLG GFIVTHSVGG GTGSGFGTLI MQNIRKEYPN T PLLSFSIY PSPRISDVLT EPYNAIFSSY RLVRDTSCSI IYDNDALYTI CQNLGIAEPT YSDLNKLISQ SMVNITAGMR FV GTLNLDL RKLITNLVPH PRLHFLMTST APLVESGGFD SQSIEKTAEV LFEKSNIQAQ VNTEDGAYIS TTVLFRGNVN PAD MDTALR AMKQKLKFVS FIPTGFKTGL SATAPNNMEF AAALVANHTG ITQVFKRILG QFDKLWSRKA FSHWYTDSGL TEED IVNAR NDIAKLVEEY EETLKFKSKD KSGEEVAAAE IAENK

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 16 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration2.3 mg/mL
BufferpH: 6.8
Details: 100mM K-PIPES 10% glycerol 10 mM K-Phosphate 0.5 mM EGTA 0.5 mM MgSO4 2 mM GTP
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4213 / 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: 1.9000000000000001 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2341375
CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Empty cylinder generated by relion_helix_toolbox
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 223429
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 150000 / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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