[English] 日本語
Yorodumi
- EMDB-69802: Heimdallarchaeales alpha/beta tubulin microtubule with three seams -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-69802
TitleHeimdallarchaeales alpha/beta tubulin microtubule with three seams
Map data
Sample
  • Complex: Heimdallarchaeales alpha/beta tubulin microtubule with three seams
    • 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.9 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 19, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_69802.png

Downloads & links

-
Map

FileDownload / File: emd_69802.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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-0.0072250227 - 0.017558632
Average (Standard dev.)0.00025086038 (±0.0011821534)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_69802_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_69802_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heimdallarchaeales alpha/beta tubulin microtubule with three seams

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

-
Supramolecule #1: Heimdallarchaeales alpha/beta tubulin microtubule with three seams

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

-
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

-
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

-
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

-
Macromolecule #4: MAGNESIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
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
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP

-
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 opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 0.3 µm / Illumination 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

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 83.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.73 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 71307
CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 2341375 / Software - Name: RELION (ver. 5.0)
Startup modelType of model: OTHER / Details: Empty cylinder generated by relion_helix_toolbox
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more