5WHH | pdb_00005whh

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 (Depositor), 0.287 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 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: https://doi.org/10.1016/j.str.2017.11.016
  • Primary Citation Related Structures: 
    5WHH, 5WHI

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 20.69 kDa 
  • Atom Count: 1,326 
  • Modeled Residue Count: 160 
  • Deposited Residue Count: 177 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bcl-2-related protein A1161Homo sapiensMutation(s): 2 
Gene Names: BCL2A1BCL2L5BFL1GRSHBPA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16548 (Homo sapiens)
Explore Q16548 
Go to UniProtKB:  Q16548
PHAROS:  Q16548
GTEx:  ENSG00000140379 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16548
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
(AQ7)T(0EH)LRRFGD(MK8)INFRQ(NH2)16synthetic constructMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
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 (Depositor), 0.287 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.71α = 90
b = 86.71β = 90
c = 40.36γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations