4I4T

Crystal structure of tubulin-RB3-TTL-Zampanolide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents.

Prota, A.E., Bargsten, K., Zurwerra, D., Field, J.J., Diaz, J.F., Altmann, K.H., Steinmetz, M.O.

(2013) Science 339: 587-590

  • DOI: 10.1126/science.1230582
  • Primary Citation of Related Structures:  
    4I4T, 4I50, 4I55

  • PubMed Abstract: 

    • Microtubule-stabilizing agents (MSAs) are efficacious chemotherapeutic drugs widely used for the treatment of cancer. Despite the importance of MSAs for medical applications and basic research, their molecular mechanisms of action on tubulin and microtubules remain elusive ...

    Microtubule-stabilizing agents (MSAs) are efficacious chemotherapeutic drugs widely used for the treatment of cancer. Despite the importance of MSAs for medical applications and basic research, their molecular mechanisms of action on tubulin and microtubules remain elusive. We determined high-resolution crystal structures of αβ-tubulin in complex with two unrelated MSAs, zampanolide and epothilone A. Both compounds were bound to the taxane pocket of β-tubulin and used their respective side chains to induce structuring of the M-loop into a short helix. Because the M-loop establishes lateral tubulin contacts in microtubules, these findings explain how taxane-site MSAs promote microtubule assembly and stability. Further, our results offer fundamental structural insights into the control mechanisms of microtubule dynamics.

    Related Citations: 
    • Structural basis of tubulin tyrosination by tubulin tyrosine ligase.
      Prota, A.E., Magiera, M.M., Kuijpers, M., Bargsten, K., Frey, D., Wieser, M., Jaussi, R., Hoogenraad, C.C., Kammerer, R.A., Janke, C., Steinmetz, M.O.
      (2013) J Cell Biol 200: 259
    Organizational Affiliation: 

    Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA, C450Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups  
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UniProt GroupP81947
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-2B chainB, D445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus)
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Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups  
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UniProt GroupP63043
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin Tyrosine ligase, TTLF384Gallus gallusMutation(s): 0 
Gene Names: TTL
UniProt
Find proteins for E1BQ43 (Gallus gallus)
Explore E1BQ43 
Go to UniProtKB:  E1BQ43
Entity Groups  
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UniProt GroupE1BQ43
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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G [auth A],
V [auth C]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ACP
Query on ACP
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DA [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N		 Ligand Interaction
ZPN
Query on ZPN
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AA [auth D](2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide
C29 H39 N O6
KNEMNZWQWFRUIB-KZVIXHMTSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
O [auth B],
Y [auth D]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MES
Query on MES
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U [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
TYR
Query on TYR
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T [auth B]TYROSINE
C9 H11 N O3
OUYCCCASQSFEME-QMMMGPOBSA-N		 Ligand Interaction
GOL
Query on GOL
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EA [auth F],
FA [auth F],
L [auth A],
M [auth A],
N [auth A],
EA [auth F],
FA [auth F],
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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I [auth A],
K [auth A],
Q [auth B],
X [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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BA [auth F],
CA [auth F],
H [auth A],
P [auth B],
W [auth C],
BA [auth F],
CA [auth F],
H [auth A],
P [auth B],
W [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.77α = 90
b = 158.64β = 90
c = 179.24γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Database references
  • Version 1.2: 2013-02-20
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description