7EVB | pdb_00007evb

Deposited: 2021-05-21 Released: 2022-03-23
Deposition Author(s): Robinson, R.C., Akil, C.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Simons Foundation, Other private

Experimental Data Snapshot

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

(2022) Sci Adv 8: eabm2225-eabm2225

PubMed: 35333570 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abm2225
Primary Citation Related Structures:
7EVB, 7EVC, 7EVD, 7EVE, 7EVG, 7EVH, 7EVI, 7EVK, 7EVL, 7F1A, 7F1B

PubMed Abstract:
Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.

Organizational Affiliation

Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-like protein	A [auth B]	425	Candidatus Odinarchaeum yellowstonii	Mutation(s): 1 Gene Names: cetZ, OdinLCB4_01330

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain B Interactions & Density Focus chain B
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
NA (Subject of Investigation/LOI) Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B]	D [auth B], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Software Package:

& Funding Information

Deposition Author(s):

Robinson, R.C.

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR19S5
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H00476
Simons Foundation	United States	GBMF9743
Other private	United States	Moore Foundation GBMF9743