4I4T

Crystal structure of tubulin-RB3-TTL-Zampanolide complex

• PDB DOI: https://doi.org/10.2210/pdb4I4T/pdb

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


• Deposited: 2012-11-28 Released: 2013-01-23 
• Deposition Author(s): Prota, A.E., Steinmetz, M.O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.204 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 

Starting Models: experimental

Literature

Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents.

Prota, A.E., Bargsten, K., Zurwerra, D., Field, J.J., Diaz, J.F., Altmann, K.H., Steinmetz, M.O.

(2013) Science 339: 587-590

• PubMed: 23287720 
• DOI: https://doi.org/10.1126/science.1230582
• Primary Citation of Related Structures:  
  4I4T, 4I50, 4I55


• PubMed Abstract: 
  

  Microtubule-stabilizing agents (MSAs) are efficacious chemotherapeutic drugs widely used for the treatment of cancer. Despite the importance of MSAs for medical applications and basic research, their molecular mechanisms of action on tubulin and microtubules remain elusive. We determined high-resolution crystal structures of αβ-tubulin in complex with two unrelated MSAs, zampanolide and epothilone A. Both compounds were bound to the taxane pocket of β-tubulin and used their respective side chains to induce structuring of the M-loop into a short helix. Because the M-loop establishes lateral tubulin contacts in microtubules, these findings explain how taxane-site MSAs promote microtubule assembly and stability. Further, our results offer fundamental structural insights into the control mechanisms of microtubule dynamics.

---

Organizational Affiliation: 

Biomolecular Research, Paul Scherrer Institut, Villigen PSI, 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.

Macromolecule Content

• Total Structure Weight: 265.6 kDa 
• Atom Count: 19,745 
• Modelled Residue Count: 2,218 
• Deposited Residue Count: 2,317 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	450	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, TTL	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], V [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	DA [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
ZPN	AA [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	O [auth B], Y [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES	U [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
TYR	T [auth B]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
GOL	EA [auth F], FA [auth F], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], K [auth A], Q [auth B], X [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	BA [auth F], CA [auth F], H [auth A], P [auth B], W [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.204 
• R-Value Work: 0.171 
• R-Value Observed: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.77	α = 90
b = 158.64	β = 90
c = 179.24	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Prota, A.E., Steinmetz, M.O.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2013-02-20
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description