1TVK | pdb_00001tvk

The binding mode of epothilone A on a,b-tubulin by electron crystallography

• PDB DOI: https://doi.org/10.2210/pdb1TVK/pdb

• Classification: CELL CYCLE, STRUCTURAL PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2004-06-29 Released: 2004-09-14 
• Deposition Author(s): Nettles, J.H., Li, H., Cornett, B., Krahn, J.M., Snyder, J.P., Downing, K.H.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.89 Å
• R-Value Free: 
  0.321 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.333 (Depositor), 0.314 (DCC) 
• R-Value Observed: 
  0.332 (Depositor) 

Starting Model: experimental

Literature

The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography

Nettles, J.H., Li, H., Cornett, B., Krahn, J.M., Snyder, J.P., Downing, K.H.

(2004) Science 305: 866-869

• PubMed: 15297674 
• DOI: https://doi.org/10.1126/science.1099190
• Primary Citation Related Structures: 
  1TVK


• PubMed Abstract: 
  

  The structure of epothilone A, bound to alpha,beta-tubulin in zinc-stabilized sheets, was determined by a combination of electron crystallography at 2.89 angstrom resolution and nuclear magnetic resonance-based conformational analysis. The complex explains both the broad-based epothilone structure-activity relationship and the known mutational resistance profile. Comparison with Taxol shows that the longstanding expectation of a common pharmacophore is not met, because each ligand exploits the tubulin-binding pocket in a unique and independent manner.

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Organizational Affiliation: 
• Molecular and Systems Pharmacology, Emory University, Atlanta, GA 30322, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 98.27 kDa 
• Atom Count: 6,672 
• Modeled Residue Count: 838 
• Deposited Residue Count: 867 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A	440	Bos taurus	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q2HJ86 (Bos taurus) Explore Q2HJ86  Go to UniProtKB:  Q2HJ86

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B	427	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856  Go to UniProtKB:  Q6B856

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
EP	E [auth B]	EPOTHILONE A C26 H39 N O6 S HESCAJZNRMSMJG-KKQRBIROSA-N
GDP	D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.89 Å
• R-Value Free:  0.321 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.333 (Depositor), 0.314 (DCC) 
• R-Value Observed: 0.332 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.2	α = 90
b = 93.5	β = 90
c = 90	γ = 90

EM Software:

Task	Software Package	Version
RECONSTRUCTION	MRC

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-14 
Deposition Author(s): Nettles, J.H., Li, H., Cornett, B., Krahn, J.M., Snyder, J.P., Downing, K.H.

Revision History  

• Version 1.0: 2004-09-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-07-18
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description