24SV | pdb_000024sv

Averaged protofilament of Heimdallarchaeales alpha/beta tubulin microtubule with a single seam

PDB DOI: https://doi.org/10.2210/pdb24SV/pdb
EM Map EMD-69801: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Candidatus Heimdallarchaeaceae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-03-19 Released: 2026-06-24
Deposition Author(s): Tran, L.T., Ali, S., Matsumoto, T., Yamazaki, Y., Narita, A., Miyazaki, M., Robinson, R.C.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Other private, Japan Science and Technology

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure and dynamics of a four-protofilament microtubule from Heimdallarchaeales alpha/beta-tubulin

Tran, L.T., Ali, S., Matsumoto, T., Yamazaki, Y., Narita, A., Miyazaki, M., Robinson, R.C.

To be published.

Macromolecule Content

Total Structure Weight: 191.06 kDa
Atom Count: 13,112
Modeled Residue Count: 1,682
Deposited Residue Count: 1,724
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heim-alpha-tubulin	A, C	422	Candidatus Heimdallarchaeaceae	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heim-beta-tubulin	B, D	440	Candidatus Heimdallarchaeaceae	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain L [auth D]	E [auth A], G [auth B], I [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	F [auth A], H [auth B], J [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.40 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	5.0

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	25K18436
Japan Society for the Promotion of Science (JSPS)	Japan	22H05171
Japan Society for the Promotion of Science (JSPS)	Japan	23764079
Other private	Japan	2025-4021
Other private	Japan	--
Other private	Japan	500230057
Japan Science and Technology	Japan	JPMJFR2417
Other private	Japan	--