9F07

TUBULIN:STATHMIN:DARPIN:TAU MTBR3 COMPLEX

PDB DOI: https://doi.org/10.2210/pdb9F07/pdb

Classification: CELL CYCLE
Organism(s): Ovis aries, Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-04-15 Released: 2024-11-13
Deposition Author(s): Ammar Khodja, L., Campanacci, V., Gigant, b.
Funding Organization(s): Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche (ANR), French Infrastructure for Integrated Structural Biology (FRISBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.234
R-Value Work: 0.200
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The structure of a Tau fragment bound to tubulin prompts new hypotheses on Tau mechanism and oligomerization

Khodja, L.A., Campanacci, V., Lippens, G., Gigant, B.

(2024) PNAS Nexus

DOI: https://doi.org/10.1093/pnasnexus/pgae487

Macromolecule Content

Total Structure Weight: 270.17 kDa
Atom Count: 17,447
Modelled Residue Count: 2,178
Deposited Residue Count: 2,414
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A, E	451	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWZ0 (Ovis aries) Explore D0VWZ0 Go to UniProtKB: D0VWZ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWZ0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, F	445	Ovis aries	Mutation(s): 0
UniProt
Find proteins for D0VWY9 (Ovis aries) Explore D0VWY9 Go to UniProtKB: D0VWY9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VWY9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	C, G	121	Homo sapiens	Mutation(s): 3 Gene Names: STMN4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H169 (Homo sapiens) Explore Q9H169 Go to UniProtKB: Q9H169
PHAROS: Q9H169 GTEx: ENSG00000015592
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H169
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
D2-R3	D, H	190	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain U [auth E] MOL2 format, chain I [auth A] MOL2 format, chain U [auth E] mmCIF format, chain I [auth A] mmCIF format, chain U [auth E]	I [auth A], U [auth E]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain I [auth A] Focus chain U [auth E] Interactions & Density Focus chain I [auth A] Focus chain U [auth E]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain W [auth F] MOL2 format, chain K [auth B] MOL2 format, chain W [auth F] mmCIF format, chain K [auth B] mmCIF format, chain W [auth F]	K [auth B], W [auth F]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth B] Focus chain W [auth F] Interactions & Density Focus chain K [auth B] Focus chain W [auth F]
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain DA [auth H] SDF format, chain S [auth B] SDF format, chain T [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain DA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain T [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain DA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain T [auth D]	AA [auth F], BA [auth F], DA [auth H], S [auth B], T [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth H] Focus chain S [auth B] Focus chain T [auth D] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain DA [auth H] Focus chain S [auth B] Focus chain T [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain P [auth B] MOL2 format, chain CA [auth F] MOL2 format, chain P [auth B] mmCIF format, chain CA [auth F] mmCIF format, chain P [auth B]	CA [auth F], P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain P [auth B] Interactions & Density Focus chain CA [auth F] Focus chain P [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain X [auth F] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain X [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	L [auth B] M [auth B] N [auth B] O [auth B] X [auth F] L [auth B], M [auth B], N [auth B], O [auth B], X [auth F], Y [auth F], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain X [auth F] Focus chain Y [auth F] Focus chain Z [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain V [auth E] MOL2 format, chain J [auth A] MOL2 format, chain V [auth E] mmCIF format, chain J [auth A] mmCIF format, chain V [auth E]	J [auth A], V [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain V [auth E] Interactions & Density Focus chain J [auth A] Focus chain V [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.234
R-Value Work: 0.200
R-Value Observed: 0.201
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.298	α = 90
b = 222.25	β = 90
c = 227.657	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Ammar Khodja, L.

Campanacci, V.

Gigant, b.

Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	MITI
Agence Nationale de la Recherche (ANR)	France	ANR-22-CE11-0002-01
French Infrastructure for Integrated Structural Biology (FRISBI)	France	ANR-10-INBS-05