6TIS | pdb_00006tis

DROSOPHILA GDP-TUBULIN

PDB DOI: https://doi.org/10.2210/pdb6TIS/pdb

Classification: CELL CYCLE
Organism(s): Drosophila melanogaster, Rattus norvegicus
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): Yes

Deposited: 2019-11-22 Released: 2021-01-27
Deposition Author(s): Gigant, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.218 (Depositor), 0.236 (DCC)
R-Value Work:
0.183 (Depositor), 0.197 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation.

Ayukawa, R., Iwata, S., Imai, H., Kamimura, S., Hayashi, M., Ngo, K.X., Minoura, I., Uchimura, S., Makino, T., Shirouzu, M., Shigematsu, H., Sekimoto, K., Gigant, B., Muto, E.

(2021) J Cell Biol 220

PubMed: 33544140 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1083/jcb.202007033
Primary Citation Related Structures:
6TIS, 6TIU, 6TIY, 6TIZ

PubMed Abstract:
Nucleation of microtubules (MTs) is essential for cellular activities, but its mechanism is unknown because of the difficulty involved in capturing rare stochastic events in the early stage of polymerization. Here, combining rapid flush negative stain electron microscopy (EM) and kinetic analysis, we demonstrate that the formation of straight oligomers of critical size is essential for nucleation. Both GDP and GTP tubulin form single-stranded oligomers with a broad range of curvatures, but upon nucleation, the curvature distribution of GTP oligomers is shifted to produce a minor population of straight oligomers. With tubulin having the Y222F mutation in the β subunit, the proportion of straight oligomers increases and nucleation accelerates. Our results support a model in which GTP binding generates a minor population of straight oligomers compatible with lateral association and further growth to MTs. This study suggests that cellular factors involved in nucleation promote it via stabilization of straight oligomers.

Organizational Affiliation

Laboratory for Molecular Biophysics, RIKEN Center for Brain Science, Saitama, Japan.

Macromolecule Content

Total Structure Weight: 220.44 kDa
Atom Count: 15,255
Modeled Residue Count: 1,850
Deposited Residue Count: 1,937
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1 chain	A, C	450	Drosophila melanogaster	Mutation(s): 1 Gene Names: alphaTub84B, tubA84B, CG1913 EC: 3.6.5
UniProt
Find proteins for P06603 (Drosophila melanogaster) Explore P06603 Go to UniProtKB: P06603
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06603
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-1 chain	B, D	447	Drosophila melanogaster	Mutation(s): 0 Gene Names: betaTub56D, CG9277
UniProt
Find proteins for Q24560 (Drosophila melanogaster) Explore Q24560 Go to UniProtKB: Q24560
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q24560
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 3 Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus) Explore P63043 Go to UniProtKB: P63043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63043
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain F [auth A] MOL2 format, chain R [auth C] MOL2 format, chain F [auth A] mmCIF format, chain R [auth C] mmCIF format, chain F [auth A]	F [auth A], R [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain R [auth C]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain M [auth B] MOL2 format, chain U [auth D] MOL2 format, chain M [auth B] mmCIF format, chain U [auth D] mmCIF format, chain M [auth B]	M [auth B], U [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain M [auth B] Focus chain U [auth D] Interactions & Density Focus chain M [auth B] Focus chain U [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] N [auth B] H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B], T [auth C], V [auth D], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A]	L [auth A], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain G [auth A] MOL2 format, chain S [auth C] MOL2 format, chain G [auth A] mmCIF format, chain S [auth C] mmCIF format, chain G [auth A]	G [auth A], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.218 (Depositor), 0.236 (DCC)
R-Value Work: 0.183 (Depositor), 0.197 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.588	α = 90
b = 126.515	β = 90
c = 250.241	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
BUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

Gigant, B.

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2021-02-17
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description