6Y6D | pdb_00006y6d

Tubulin-7-Aminonoscapine complex

PDB DOI: https://doi.org/10.2210/pdb6Y6D/pdb

Classification: CELL CYCLE
Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-26 Released: 2020-07-22
Deposition Author(s): Oliva, M.A., Prota, A.E., Rodriguez-Salarichs, J., Gu, W., Bennani, Y.L., Jimenez-Barbero, J., Canales, A., Steinmetz, M.O., Diaz, J.F.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness, Spanish Ministry of Science, Innovation, and Universities, Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.224 (Depositor), 0.226 (DCC)
R-Value Work:
0.184 (Depositor), 0.187 (DCC)
R-Value Observed:
0.186 (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

Structural Basis of Noscapine Activation for Tubulin Binding.

Oliva, M.A., Prota, A.E., Rodriguez-Salarichs, J., Bennani, Y.L., Jimenez-Barbero, J., Bargsten, K., Canales, A., Steinmetz, M.O., Diaz, J.F.

(2020) J Med Chem 63: 8495-8501

PubMed: 32657585 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.0c00855
Primary Citation Related Structures:
6Y6D

PubMed Abstract:
Noscapine is a natural alkaloid that is used as an antitussive medicine. However, it also acts as a weak anticancer agent in certain in vivo models through a mechanism that is largely unknown. Here, we performed structural studies and show that the cytotoxic agent 7A- O -demethoxy-amino-noscapine (7A-aminonoscapine) binds to the colchicine site of tubulin. We suggest that the 7A-methoxy group of noscapine prevents binding to tubulin due to a steric clash of the compound with the T5-loop of α-tubulin. We further propose that the anticancer activity of noscapine arises from a bioactive metabolite that binds to the colchicine site of tubulin to induce mitotic arrest through a microtubule cytoskeleton-based mechanism.

Organizational Affiliation

Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu, 9, C.P. 28040 Madrid, Spain.

Macromolecule Content

Total Structure Weight: 265.36 kDa
Atom Count: 18,029
Modeled Residue Count: 2,177
Deposited Residue Count: 2,319
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947 Go to UniProtKB: P81947
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P81947
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856 Go to UniProtKB: Q6B856
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6B856
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): 0 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

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-Tyrosine Ligase	F	384	Gallus gallus	Mutation(s): 0 Gene Names: TTL

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 O [auth C] SDF format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain G [auth A]	G [auth A], O [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain O [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain U [auth F] MOL2 format, chain U [auth F] mmCIF format, chain U [auth F]	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain U [auth F] Interactions & Density Focus chain U [auth F]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain J [auth B] MOL2 format, chain R [auth D] MOL2 format, chain J [auth B] mmCIF format, chain R [auth D] mmCIF format, chain J [auth B]	J [auth B], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain J [auth B] Focus chain R [auth D] Interactions & Density Focus chain J [auth B] Focus chain R [auth D]
OBQ (Subject of Investigation/LOI) Query on OBQ Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain L [auth B] MOL2 format, chain T [auth D] MOL2 format, chain L [auth B] mmCIF format, chain T [auth D] mmCIF format, chain L [auth B]	L [auth B], T [auth D]	(3~{S})-7-azanyl-6-methoxy-3-[(5~{R})-4-methoxy-6-methyl-7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-3~{H}-2-benzofuran-1-one C₂₁ H₂₂ N₂ O₆ WPUKOXIOPURGHT-MSOLQXFVSA-N		Interactions Focus chain L [auth B] Focus chain T [auth D] Interactions & Density Focus chain L [auth B] Focus chain T [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain I [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain I [auth A]	I [auth A], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth C] SDF format, chain V [auth F] SDF format, chain S [auth D] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth C] MOL2 format, chain V [auth F] MOL2 format, chain S [auth D] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth C] mmCIF format, chain V [auth F] mmCIF format, chain S [auth D] mmCIF format, chain K [auth B]	H [auth A], K [auth B], P [auth C], S [auth D], V [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.224 (Depositor), 0.226 (DCC)
R-Value Work: 0.184 (Depositor), 0.187 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.36	α = 90
b = 157.15	β = 90
c = 180.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-22

Deposition Author(s):

Oliva, M.A.

Prota, A.E.

Rodriguez-Salarichs, J.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2013-47014-P
Spanish Ministry of Economy and Competitiveness	Spain	BFU2016-75319-R
Spanish Ministry of Science, Innovation, and Universities	Spain	RYC-2011-07900
Swiss National Science Foundation	Switzerland	31003A_166608

Revision History (Full details and data files)

Version 1.0: 2020-07-22
Type: Initial release
Version 1.1: 2020-08-26
Changes: Database references, Derived calculations
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description