5JQG

An apo tubulin-RB-TTL complex structure used for side-by-side comparison


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Pironetin reacts covalently with cysteine-316 of alpha-tubulin to destabilize microtubule

Yang, J.Wang, Y.X.Wang, T.Jiang, J.Botting, C.H.Liu, H.Chen, Q.Yang, J.Naismith, J.H.Zhu, X.Chen, L.

(2016) Nat Commun 7: 12103-12103

  • DOI: 10.1038/ncomms12103
  • Primary Citation of Related Structures:  
    5JQG, 5FNV

  • PubMed Abstract: 
  • Molecules that alter the normal dynamics of microtubule assembly and disassembly include many anticancer drugs in clinical use. So far all such therapeutics target β-tubulin, and structural biology has explained the basis of their action and permitted design of new drugs ...

    Molecules that alter the normal dynamics of microtubule assembly and disassembly include many anticancer drugs in clinical use. So far all such therapeutics target β-tubulin, and structural biology has explained the basis of their action and permitted design of new drugs. However, by shifting the profile of β-tubulin isoforms, cancer cells become resistant to treatment. Compounds that bind to α-tubulin are less well characterized and unexploited. The natural product pironetin is known to bind to α-tubulin and is a potent inhibitor of microtubule polymerization. Previous reports had identified that pironetin reacts with lysine-352 residue however analogues designed on this model had much lower potency, which was difficult to explain, hindering further development. We report crystallographic and mass spectrometric data that reveal that pironetin forms a covalent bond to cysteine-316 in α-tubulin via a Michael addition reaction. These data provide a basis for the rational design of α-tubulin targeting chemotherapeutics.


    Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy and Cancer, Chengdu 610041, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA, C451Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
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Go to UniProtKB:  Q2XVP4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB, D445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
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Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinF384Gallus gallusMutation(s): 0 
Gene Names: TTL
UniProt
Find proteins for E1BQ43 (Gallus gallus)
Explore E1BQ43 
Go to UniProtKB:  E1BQ43
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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G [auth A], P [auth C], S [auth D]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ACP
Query on ACP

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

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K [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MES
Query on MES

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N [auth B], O [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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I [auth A], M [auth B], R [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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J [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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H [auth A], L [auth B], Q [auth C], T [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.05α = 90
b = 158.12β = 90
c = 180.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection, Database references, Derived calculations