Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2CD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer -A4BC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 265603.25 
• Atom Count: 18223 
• Residue Count: 2317 
• Unique protein chains: 4

4I4T

Crystal structure of tubulin-RB3-TTL-Zampanolide complex

• DOI: 10.2210/pdb4I4T/pdb

• Classification: CELL CYCLE
• Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
• Expression System: Escherichia coli


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.204 
• R-Value Work: 0.171 

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: 10.1126/science.1230582
• Primary Citation of Related Structures:  
  4I55, 4I50


• 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.

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Related Citations: 

• Structural basis of tubulin tyrosination by tubulin tyrosine ligase.
  Prota, A.E.,Magiera, M.M.,Kuijpers, M.,Bargsten, K.,Frey, D.,Wieser, M.,Jaussi, R.,Hoogenraad, C.C.,Kammerer, R.A.,Janke, C.,Steinmetz, M.O.
  (2013) J.Cell Biol. 200: 259




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Organizational Affiliation: 

Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Tubulin alpha-1B chain	A, C	450	Bos taurus	Mutation(s): 0
Find proteins for P81947 (Bos taurus) Go to UniProtKB:  P81947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0  Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus) Go to Gene View: TUBB2B Go to UniProtKB:  Q6B856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0  Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus) Go to UniProtKB:  P63043

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Tubulin Tyrosine ligase, TTL	F	384	Gallus gallus	Mutation(s): 0  Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus) Go to Gene View: TTL Go to UniProtKB:  E1BQ43

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GDP	B, D	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
TYR	B	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
GTP	A, C	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A, B, F	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
ZPN	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 (-)-ZAMPANOLIDE (Bound form) C29 H39 N O6 KNEMNZWQWFRUIB-KZVIXHMTSA-N
MG	A, B, C, D, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ACP	F	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TYR	Ki: 25000 nM (88) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.204 
• R-Value Work: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 104.770	α = 90.00
b = 158.640	β = 90.00
c = 179.240	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-28 
• 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
  Type: Database references
• Version 1.2: 2013-02-20
  Type: Database references
• Version 1.3: 2017-11-15
  Type: Refinement description