5XLT | pdb_00005xlt

The crystal structure of tubulin in complex with 4'-demethylepipodophyllotoxin

• PDB DOI: https://doi.org/10.2210/pdb5XLT/pdb

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


• Deposited: 2017-05-11 Released: 2017-09-27 
• Deposition Author(s): Yu, Y., Chen, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Structure of 4'-demethylepipodophyllotoxin in complex with tubulin provides a rationale for drug design

Niu, L., Wang, Y., Wang, C., Wang, Y., Jiang, X., Ma, L., Wu, C., Yu, Y., Chen, Q.

(2017) Biochem Biophys Res Commun 493: 718-722

• PubMed: 28864414 
• DOI: https://doi.org/10.1016/j.bbrc.2017.08.125
• Primary Citation Related Structures: 
  5XLT


• PubMed Abstract: 
  

  Microtubules consists of αβ-tubulin heterodimers and are highly attractive targets for anti-cancer drugs. A broad range of agents have been identified to bind to tubulin and interfere with microtubule assembly, including colchicine binding site inhibitors (CBSIs). Podophyllotoxin is a CBSI that inhibits the assembly of microtubules. However, for a long time, the design and development of podophyllotoxin family drugs have been hindered by the lack of high-resolution structural information of the tubulin-agent complex. We report the first high-resolution (2.8 Å) structure of a podophyllotoxin family agent (4'-demethylepipodophyllotoxin, DMEP) complexed with tubulin and revealed the detailed interactions between DMEP and tubulin. Comparison of this structure and other CBSIs explains previous results of the structure-activity-relationship (SAR) studies, and provides insights into the development of new podophyllotoxin derivatives targeting the colchicine site.

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Organizational Affiliation: 
• Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China.
Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China; Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Street, Chengdu, Sichuan, 610041, PR China.
Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Street, Chengdu, Sichuan, 610041, PR China.
Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Street, Chengdu, Sichuan, 610041, PR China; National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guo Xue Street, Chengdu, Sichuan, 610041, PR China.
Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China. Electronic address: [e-mail].
Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center of Biotherapy, Chengdu, 610041, PR China. Electronic address: [e-mail].

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: 265.11 kDa 
• Atom Count: 17,615 
• Modeled Residue Count: 2,180 
• 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	F	384	Gallus gallus	Mutation(s): 0  Gene Names: TTL

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	G [auth A], O [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	U [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	J [auth B], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
89O	N [auth B], S [auth D]	(5S,5aR,8aR,9R)-9-(3,5-dimethoxy-4-oxidanyl-phenyl)-5-oxidanyl-5a,6,8a,9-tetrahydro-5H-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one C21 H20 O8 YVCVYCSAAZQOJI-JHQYFNNDSA-N
MES	L [auth B], M [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA	I [auth A], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth A], K [auth B], P [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.473	α = 90
b = 156.926	β = 90
c = 180.868	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-27 
Deposition Author(s): Yu, Y., Chen, Q.

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations