5NG1 | pdb_00005ng1

TUBULIN-MTC-zampanolide complex

• PDB DOI: https://doi.org/10.2210/pdb5NG1/pdb

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


• Deposited: 2017-03-16 Released: 2017-10-25 
• Deposition Author(s): Field, J.J., Pera, B., Estevez Gallego, J., Calvo, E., Rodriguez-Salarichs, J., Saez-Calvo, G., Zuwerra, D., Jordi, M., Prota, A.E., Menchon, G., Miller, J.H., Altmann, K.-H., Diaz, J.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites.

Field, J.J., Pera, B., Gallego, J.E., Calvo, E., Rodriguez-Salarichs, J., Saez-Calvo, G., Zuwerra, D., Jordi, M., Andreu, J.M., Prota, A.E., Menchon, G., Miller, J.H., Altmann, K.H., Diaz, J.F.

(2018) J Nat Prod 81: 494-505

• PubMed: 29023132 
• DOI: https://doi.org/10.1021/acs.jnatprod.7b00704
• Primary Citation Related Structures: 
  5NFZ, 5NG1


• PubMed Abstract: 
  

  The marine natural product zampanolide and analogues thereof constitute a new chemotype of taxoid site microtubule-stabilizing agents with a covalent mechanism of action. Zampanolide-ligated tubulin has the switch-activation loop (M-loop) in the assembly prone form and, thus, represents an assembly activated state of the protein. In this study, we have characterized the biochemical properties of the covalently modified, activated tubulin dimer, and we have determined the effect of zampanolide on tubulin association and the binding of tubulin ligands at other binding sites. Tubulin activation by zampanolide does not affect its longitudinal oligomerization but does alter its lateral association properties. The covalent binding of zampanolide to β-tubulin affects both the colchicine site, causing a change of the quantum yield of the bound ligand, and the exchangeable nucleotide binding site, reducing the affinity for the nucleotide. While these global effects do not change the binding affinity of 2-methoxy-5-(2,3,4-trimethoxyphenyl)-2,4,6-cycloheptatrien-1-one (MTC) (a reversible binder of the colchicine site), the binding affinity of a fluorescent analogue of GTP (Mant-GTP) at the nucleotide E-site is reduced from 12 ± 2 × 10 ⁵ M ^-1 in the case of unmodified tubulin to 1.4 ± 0.3 × 10 ⁵ M ^-1 in the case of the zampanolide tubulin adduct, indicating signal transmission between the taxane site and the colchicine and nucleotide sites of β-tubulin.

---

Organizational Affiliation: 
• Centre for Biodiscovery, School of Biological Sciences , Victoria University of Wellington , Wellington 6012 , New Zealand.
Centro de Investigaciones Biológicas (CIB) , CSIC , Madrid 28048 , Spain.
Unidad de Proteómica , Centro Nacional de Investigaciones Cardiovasculares , Madrid 28029 , Spain.
Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) Zürich, Institute of Pharmaceutical Sciences , HCI H405, Zürich 8092 , Switzerland.
Laboratory of Biomolecular Research , Paul Scherrer Institut , Villigen PSI 5232 , Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 266.16 kDa 
• Atom Count: 18,369 
• Modeled Residue Count: 2,207 
• Deposited Residue Count: 2,319 
• Unique protein chains: 4

Macromolecules

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 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 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 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 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	G [auth A], P [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	W [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
8WE	M [auth B]	(2~{Z},4~{E})-~{N}-[(~{S})-oxidanyl-[(1~{S},2~{E},5~{S},11~{R},17~{S},19~{R})-3,11,19-trimethyl-7,13-bis(oxidanylidene)-6,21-dioxabicyclo[15.3.1]henicos-2-en-5-yl]methyl]hexa-2,4-dienamide C29 H45 N O6 WSHDEXCLDGAKJW-NFPHSYLMSA-N
ZPN	V [auth D]	(2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide C29 H39 N O6 KNEMNZWQWFRUIB-KZVIXHMTSA-N
GDP	J [auth B], S [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
8WB	L [auth B], U [auth D]	2-methoxy-5-(2,3,4-trimethoxyphenyl)cyclohepta-2,4,6-trien-1-one C17 H18 O5 QIMGSZURBOTPMW-UHFFFAOYSA-N
MES	O [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], R [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth A], K [auth B], Q [auth C], T [auth D], X [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.237	α = 90
b = 157.418	β = 90
c = 178.858	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Field, J.J., Pera, B., Estevez Gallego, J., Calvo, E., Rodriguez-Salarichs, J., Saez-Calvo, G., Zuwerra, D., Jordi, M., Prota, A.E., Menchon, G., Miller, J.H., Altmann, K.-H., Diaz, J.F.

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2018-04-04
  Changes: Data collection, Database references
• Version 1.2: 2018-05-02
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary