8WD0

Crystal structure of T2R-TTL-Erianin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

Starting Model: experimental
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Literature

The cytotoxic natural compound erianin binds to colchicine site of beta-tubulin and overcomes taxane resistance

Yan, W.Zhou, Y.Yuan, X.Bai, P.Tang, M.Chen, L.Wei, H.Yang, J.

(2024) Bioorg Chem 150: 107569

  • DOI: https://doi.org/10.1016/j.bioorg.2024.107569
  • Primary Citation of Related Structures:  
    8WD0

  • PubMed Abstract: 

    Erianin, a natural compound derived from Dendrobium, has shown significant anticancer properties against a wide range of cancer cells. Despite the identification of multiple mechanisms of action for erianin, none of these mechanisms fully account for its broad-spectrum effect. In this study, we aimed to identify the cellular target and underlying mechanism responsible for the broad-spectrum antitumor effects of erianin. We found that erianin effectively inhibited tubulin polymerization in cancer cells and purified tubulin. Through competition binding assays and X-ray crystallography, it was revealed that erianin bound to the colchicine site of β-tubulin. Importantly, the X-ray crystal structure of the tubulin-erianin complex was solved, providing clear insight into the orientation and position of erianin in the colchicine-binding site. Erianin showed activity against paclitaxel-resistant cells, evidenced by G2/M cell cycle arrest, apoptosis-related PARP and Caspase-3 cleavage, and in vivo xenograft studies. The study concluded that erianin bound reversibly to the colchicine site of β-tubulin, inhibited tubulin polymerization, and displayed anticancer activity against paclitaxel-resistant cells, offering valuable insights for further exploration as potential anticancer agents.


  • Organizational Affiliation

    Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China. Electronic address: yanxiaowei369@sina.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
451Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
445Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AGU7 (Sus scrofa)
Explore A0A287AGU7 
Go to UniProtKB:  A0A287AGU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287AGU7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4189Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63043
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin tyrosine ligase380Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A8V0Z8P0 (Gallus gallus)
Explore A0A8V0Z8P0 
Go to UniProtKB:  A0A8V0Z8P0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8V0Z8P0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C],
R [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP
Query on ACP

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U [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP
Query on GDP

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N [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
W4F (Subject of Investigation/LOI)
Query on W4F

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M [auth B],
T [auth D]
2-methoxy-5-[2-(3,4,5-trimethoxyphenyl)ethyl]phenol
C18 H22 O5
UXDFUVFNIAJEGM-UHFFFAOYSA-N
MES
Query on MES

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L [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL
Query on GOL

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J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

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I [auth A],
Q [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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H [auth A],
K [auth B],
P [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
W4F BindingDB:  8WD0 IC50: 630 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.56α = 90
b = 181.54β = 90
c = 104.74γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-07-03 
  • Deposition Author(s): Yang, J.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release