Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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)

Macromolecule Content

• Total Structure Weight: 265.73 kDa 
• Atom Count: 19585 
• Residue Count: 2210 
• Unique protein chains: 4

5LXT

Tubulin-Discodermolide complex

• DOI: 10.2210/pdb5LXT/pdb

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


• Deposited: 2016-09-22 Released: 2017-03-01 
• Deposition Author(s): Prota, A.E., Steinmetz, M.O.
• Funding Organization(s): Swiss National Science Foundation, Spanish Ministry of Economy and Competitiveness, National Cancer Institute, Breast Cancer Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Structural Basis of Microtubule Stabilization by Discodermolide.

Prota, A.E., Bargsten, K., Redondo-Horcajo, M., Smith, A.B., Yang, C.H., McDaid, H.M., Paterson, I., Horwitz, S.B., Fernando Diaz, J., Steinmetz, M.O.

(2017) Chembiochem 18: 905-909

• PubMed: 28207984 
• DOI: 10.1002/cbic.201600696
• Primary Citation of Related Structures:  
  5LXT, 5LXS


• PubMed Abstract: 
  

Microtubule-stabilizing agents (MSAs) are widely used in chemotherapy. Using X-ray crystallography we elucidated the detailed binding modes of two potent MSAs, (+)-discodermolide (DDM) and the DDM-paclitaxel hybrid KS-1-199-32, in the taxane pocket of β-tubulin. The two compounds bind in a very similar hairpin conformation, as previously observed in solution. However, they stabilize the M-loop of β-tubulin differently: KS-1-199-32 induces an M-loop helical conformation that is not observed for DDM. In the context of the microtubule structure, both MSAs connect the β-tubulin helices H6 and H7 and loop S9-S10 with the M-loop. This is similar to the structural effects elicited by epothilone A, but distinct from paclitaxel. Together, our data reveal differential binding mechanisms of DDM and KS-1-199-32 on tubulin.

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Organizational Affiliation: 

Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, OFLC/111, 5232, Villigen PSI, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0
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  Gene Names: TUBB2B
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
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
Find proteins for E1BQ43 (Gallus gallus) Explore E1BQ43  Go to UniProtKB:  E1BQ43

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7AK	B, D	(+)-Discodermolide C33 H55 N O8 AADVCYNFEREWOS-OBRABYBLSA-N
GTP	A, C	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	F	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	B, D	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	A, B, C, D, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
7AK	Ka:  8720000000   M^-1  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.5	α = 90
b = 157.79	β = 90
c = 180.23	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-22 
• Released Date: 2017-03-01 
Deposition Author(s): Prota, A.E., Steinmetz, M.O.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_138659 and 31003A_166608
Spanish Ministry of Economy and Competitiveness	Spain	BIO2013-42984-R and S2010/BMD-2457 BIPEDD2
National Cancer Institute	United States	CA077263
Breast Cancer Research Foundation	United States	--

Revision History 

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence