5WHH

Crystal Structure of Bcl-2-related protein A1 in complex with stapled peptide (AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structures of Anti-apoptotic BFL-1 and Its Complex with a Covalent Stapled Peptide Inhibitor.

Harvey, E.P.Seo, H.S.Guerra, R.M.Bird, G.H.Dhe-Paganon, S.Walensky, L.D.

(2018) Structure 26: 153-160.e4

  • DOI: 10.1016/j.str.2017.11.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • BCL-2 family proteins are high-priority cancer targets whose structures provide essential blueprints for drug design. Whereas numerous structures of anti-apoptotic BCL-2 protein complexes with α-helical BH3 peptides have been reported, the correspond ...

    BCL-2 family proteins are high-priority cancer targets whose structures provide essential blueprints for drug design. Whereas numerous structures of anti-apoptotic BCL-2 protein complexes with α-helical BH3 peptides have been reported, the corresponding panel of apo structures remains incomplete. Here, we report the crystal structure of apo BFL-1 at 1.69-Å resolution, revealing similarities and key differences among unliganded anti-apoptotic proteins. Unlike all other BCL-2 proteins, apo BFL-1 contains a surface-accessible cysteine within its BH3-binding groove, allowing for selective covalent targeting by a NOXA BH3-based stapled peptide inhibitor. The crystal structure of this complex demonstrated the sulfhydryl bond and fortuitous interactions between the acrylamide-bearing moiety and a newly formed hydrophobic cavity. Comparison of the apo and BH3-liganded structures further revealed an induced conformational change. The two BFL-1 structures expand our understanding of the surface landscapes available for therapeutic targeting so that the apoptotic blockades of BFL-1-dependent cancers can be overcome.


    Organizational Affiliation

    Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address: loren_walensky@dfci.harvard.edu.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address: dhepag@crystal.harvard.edu.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bcl-2-related protein A1
A
161Homo sapiensMutation(s): 2 
Gene Names: BCL2A1 (BCL2L5, BFL1, GRS, HBPA1)
Find proteins for Q16548 (Homo sapiens)
Go to Gene View: BCL2A1
Go to UniProtKB:  Q16548
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
(AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)
B
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

AQ7
Query on AQ7
B
NON-POLYMERC12 H20 N2 O4

--

0EH
Query on 0EH
B
D-PEPTIDE LINKINGC10 H21 N O2

--

MK8
Query on MK8
B
L-peptide linkingC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 86.710α = 90.00
b = 86.710β = 90.00
c = 40.360γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release