6O0M

crystal structure of BCL-2 F104L mutation with venetoclax


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structures of BCL-2 in complex with venetoclax reveal the molecular basis of resistance mutations.

Birkinshaw, R.W.Gong, J.N.Luo, C.S.Lio, D.White, C.A.Anderson, M.A.Blombery, P.Lessene, G.Majewski, I.J.Thijssen, R.Roberts, A.W.Huang, D.C.S.Colman, P.M.Czabotar, P.E.

(2019) Nat Commun 10: 2385-2385

  • DOI: https://doi.org/10.1038/s41467-019-10363-1
  • Primary Citation of Related Structures:  
    6O0K, 6O0L, 6O0M, 6O0O, 6O0P

  • PubMed Abstract: 

    Venetoclax is a first-in-class cancer therapy that interacts with the cellular apoptotic machinery promoting apoptosis. Treatment of patients suffering chronic lymphocytic leukaemia with this BCL-2 antagonist has revealed emergence of a drug-selected BCL-2 mutation (G101V) in some patients failing therapy. To understand the molecular basis of this acquired resistance we describe the crystal structures of venetoclax bound to both BCL-2 and the G101V mutant. The pose of venetoclax in its binding site on BCL-2 reveals small but unexpected differences as compared to published structures of complexes with venetoclax analogues. The G101V mutant complex structure and mutant binding assays reveal that resistance is acquired by a knock-on effect of V101 on an adjacent residue, E152, with venetoclax binding restored by a E152A mutation. This provides a framework for considering analogues of venetoclax that might be effective in combating this mutation.


  • Organizational Affiliation

    Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. birkinshaw.r@wehi.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2166Homo sapiensMutation(s): 1 
Gene Names: BCL2BCL2L1BCL2LBCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
GTEx:  ENSG00000171791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ07817P10415
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.69α = 90
b = 48.27β = 90
c = 87.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted LBMClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.0: 2019-11-20
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-11
    Changes: Advisory, Derived calculations, Structure summary
  • Version 2.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary