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- EMDB-56154: AtubAB mini microtubule in situ in E. coli by subtomogram averaging -

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Basic information

Entry
Database: EMDB / ID: EMD-56154
TitleAtubAB mini microtubule in situ in E. coli by subtomogram averaging
Map dataAtubAB mini microtubule in situ in E. coli
Sample
  • Complex: AtubAB mini microtubule, pseudo helical
    • Protein or peptide: AtubA
    • Protein or peptide: AtubB
KeywordsMicrotubules / BtubAB / cytoskeleton / asgard archaea / eukaryogenesis / UNKNOWN FUNCTION
Biological speciesunidentified (others)
Methodsubtomogram averaging / cryo EM / Resolution: 6.4 Å
AuthorsMcAndrew MBL / Lowe J
Funding support United Kingdom, 4 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56154.png

Downloads & links

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Map

FileDownload / File: emd_56154.map.gz / Format: CCP4 / Size: 36.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtubAB mini microtubule in situ in E. coli
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 212 pix.
= 320.968 Å		1.51 Å/pix.
x 212 pix.
= 320.968 Å		1.51 Å/pix.
x 212 pix.
= 320.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.514 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.11072802 - 10.901973
Average (Standard dev.)0.13793252 (±0.8061345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions212212212
Spacing212212212
CellA=B=C: 320.96802 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56154_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map postprocessed in RELION

Fileemd_56154_additional_1.map
AnnotationMap postprocessed in RELION
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_56154_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_56154_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtubAB mini microtubule, pseudo helical

EntireName: AtubAB mini microtubule, pseudo helical
Components
  • Complex: AtubAB mini microtubule, pseudo helical
    • Protein or peptide: AtubA
    • Protein or peptide: AtubB

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Supramolecule #1: AtubAB mini microtubule, pseudo helical

SupramoleculeName: AtubAB mini microtubule, pseudo helical / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 94 kDa/nm

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Macromolecule #1: AtubA

MacromoleculeName: AtubA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSEVVVVAVG QAGNQIADQF WQLIAQEHKI GLDGMPTNGE PTGRTDVFFR KVSNRYVPRA VLVDLEPAVL KSVSDDAKPN FYDPKNKVHG ADGAGNNFAV GHTEMGAQY LEQVIGKIKN EVEKTDSLGG FIVTHSVGGG TGSGFGTLIM QNIRKEYPNT PLLSFSIYPS ...String:
MSEVVVVAVG QAGNQIADQF WQLIAQEHKI GLDGMPTNGE PTGRTDVFFR KVSNRYVPRA VLVDLEPAVL KSVSDDAKPN FYDPKNKVHG ADGAGNNFAV GHTEMGAQY LEQVIGKIKN EVEKTDSLGG FIVTHSVGGG TGSGFGTLIM QNIRKEYPNT PLLSFSIYPS PRISDVLTEP YNAIFSSYRL VRDTSCSIIY D NDALYTIC QNLGIAEPTY SDLNKLISQS MVNITAGMRF VGTLNLDLRK LITNLVPHPR LHFLMTSTAP LVESGGFDSQ SIEKTAEVLF EKSNIQAQVN TE DGAYIST TVLFRGNVNP ADMDTALRAM KQKLKFVSFI PTGFKTGLSA TAPNNMEFAA ALVANHTGIT QVFKRILGQF DKLWSRKAFS HWYTDSGLTE EDI VNARND IAKLVEEYEE TLKFKSKDKS GEEVAAAEIA ENK

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Macromolecule #2: AtubB

MacromoleculeName: AtubB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSREIISIHV GQAGLQVGAA FWRTVLEEHG LGNDGSVVDA SKEKSAVYFK QAGNNKFVPR AILVDLEPMV IKTIMNDLPG LFDPAYTIHG QSGAANNWAR GYRGADGEV NVDDVLKIVE KAVSETDSLQ GFSISHSIGG GTGSGLGSQI LKKLKETYPK YPIITFSVFP ...String:
MSREIISIHV GQAGLQVGAA FWRTVLEEHG LGNDGSVVDA SKEKSAVYFK QAGNNKFVPR AILVDLEPMV IKTIMNDLPG LFDPAYTIHG QSGAANNWAR GYRGADGEV NVDDVLKIVE KAVSETDSLQ GFSISHSIGG GTGSGLGSQI LKKLKETYPK YPIITFSVFP SPLISDAVTE PYNSVFALDH LIEYADETIV L DNHALYNL TKNNMGIKSP SYADLNKIIS WVMSGVTASL RFKGDLNTDL KELLVNLVPF PRQHFLTSTF SPIKNGTGSF EEVTTHDIIN QLFDPNNAMS DT NFDEGAY IASVVMMRGH EVKTNAVNSS LAEIKGKLRF SEFIPTGIKT GVTSETLVGF ESTGLNLSNH TGITKVFKRL AAQFDAMYER DAFVHWYLGE GMS KDDMEK ARENLGKLTT EYDTSV

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 4.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.248 Å
Applied symmetry - Helical parameters - Δ&Phi: -89.824 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 15362
ExtractionNumber tomograms: 50 / Number images used: 27734 / Software - Name: RELION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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