9G0P

Xenopus laevis undecorated microtubule - 14 protofilament, 3-start helix

PDB DOI: https://doi.org/10.2210/pdb9G0P/pdb
EM Map EMD-50942: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Xenopus laevis
Mutation(s): No

Deposited: 2024-07-08 Released: 2025-01-15
Deposition Author(s): Troman, L.A., Moores, C.A.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Mechanistic basis of temperature adaptation in microtubule dynamics across frog species

Troman, L.A., de Gaulejac, E., Moores, C.A., Reber, S.

(2025) Current Biology 35: 1-17

DOI: https://doi.org/10.1016/j.cub.2024.12.022

Macromolecule Content

Total Structure Weight: 605.83 kDa
Atom Count: 40,920
Modelled Residue Count: 5,172
Deposited Residue Count: 5,364
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-4 chain	A, B, C, D, E A, B, C, D, E, F	445	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P30883 (Xenopus laevis) Explore P30883 Go to UniProtKB: P30883
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30883
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	G [auth a] H [auth b] I [auth c] J [auth d] K [auth e] G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], L [auth f]	449	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for A0A8J0UQF0 (Xenopus laevis) Explore A0A8J0UQF0 Go to UniProtKB: A0A8J0UQF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8J0UQF0
Sequence Annotations Expand
Reference Sequence

Small Molecules

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 BA [auth e] SDF format, chain DA [auth f] SDF format, chain S [auth a] SDF format, chain U [auth b] SDF format, chain X [auth c] SDF format, chain Z [auth d] MOL2 format, chain BA [auth e] MOL2 format, chain DA [auth f] MOL2 format, chain S [auth a] MOL2 format, chain U [auth b] MOL2 format, chain X [auth c] MOL2 format, chain Z [auth d] mmCIF format, chain BA [auth e] mmCIF format, chain DA [auth f] mmCIF format, chain S [auth a] mmCIF format, chain U [auth b] mmCIF format, chain X [auth c] mmCIF format, chain Z [auth d]	BA [auth e] DA [auth f] S [auth a] U [auth b] X [auth c] BA [auth e], DA [auth f], S [auth a], U [auth b], X [auth c], Z [auth d]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BA [auth e] Focus chain DA [auth f] Focus chain S [auth a] Focus chain U [auth b] Focus chain X [auth c] Focus chain Z [auth d] Interactions & Density Focus chain BA [auth e] Focus chain DA [auth f] Focus chain S [auth a] Focus chain U [auth b] Focus chain X [auth c] Focus chain Z [auth d]
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth F]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth e] SDF format, chain CA [auth f] SDF format, chain T [auth a] SDF format, chain V [auth b] SDF format, chain W [auth c] SDF format, chain Y [auth d] MOL2 format, chain AA [auth e] MOL2 format, chain CA [auth f] MOL2 format, chain T [auth a] MOL2 format, chain V [auth b] MOL2 format, chain W [auth c] MOL2 format, chain Y [auth d] mmCIF format, chain AA [auth e] mmCIF format, chain CA [auth f] mmCIF format, chain T [auth a] mmCIF format, chain V [auth b] mmCIF format, chain W [auth c] mmCIF format, chain Y [auth d]	AA [auth e] CA [auth f] T [auth a] V [auth b] W [auth c] AA [auth e], CA [auth f], T [auth a], V [auth b], W [auth c], Y [auth d]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth e] Focus chain CA [auth f] Focus chain T [auth a] Focus chain V [auth b] Focus chain W [auth c] Focus chain Y [auth d] Interactions & Density Focus chain AA [auth e] Focus chain CA [auth f] Focus chain T [auth a] Focus chain V [auth b] Focus chain W [auth c] Focus chain Y [auth d]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Troman, L.A.

Moores, C.A.

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/R000352/1
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/Y000633/1
Wellcome Trust	United Kingdom	202679/Z/16/Z
Wellcome Trust	United Kingdom	206166/Z/17/Z