5UUL

Human Bfl-1 in complex with PUMA BH3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1.

Jenson, J.M.Ryan, J.A.Grant, R.A.Letai, A.Keating, A.E.

(2017) Elife 6

  • DOI: 10.7554/eLife.25541
  • Primary Citation of Related Structures:  
    5UUM, 5UUP, 5UUL, 5UUK

  • PubMed Abstract: 
  • Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not av ...

    Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.


    Organizational Affiliation

    Department of Biology, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-related protein A1A152Homo sapiensMutation(s): 0 
Gene Names: BCL2A1BCL2L5BFL1GRSHBPA1
Find proteins for Q16548 (Homo sapiens)
Explore Q16548 
Go to UniProtKB:  Q16548
NIH Common Fund Data Resources
PHAROS  Q16548
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-binding component 3B25Homo sapiensMutation(s): 2 
Gene Names: BBC3PUMA
Find proteins for Q9BXH1 (Homo sapiens)
Explore Q9BXH1 
Go to UniProtKB:  Q9BXH1
NIH Common Fund Data Resources
PHAROS  Q9BXH1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.213α = 90
b = 43.428β = 114.39
c = 47.384γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM110048

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence