5UUK

Human Bfl-1 in complex with a Bfl-1-specific selected peptide

• PDB DOI:  https://doi.org/10.2210/pdb5UUK/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-17 Released: 2017-06-21 
• Deposition Author(s): Jenson, J.M., Grant, R.A., Keating, A.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.163 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 

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

• PubMed: 28594323 
• DOI: https://doi.org/10.7554/eLife.25541
• Primary Citation of Related Structures:  
  5UUK, 5UUL, 5UUM, 5UUP


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 20.29 kDa 
• Atom Count: 1,604 
• Modelled Residue Count: 175 
• Deposited Residue Count: 177 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-related protein A1	A	152	Homo sapiens	Mutation(s): 0  Gene Names: BCL2A1, BCL2L5, BFL1, GRS, HBPA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16548 (Homo sapiens) Explore Q16548  Go to UniProtKB:  Q16548
PHAROS:  Q16548

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bfl-1-specific selected peptide	B	25	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.163 
• R-Value Work: 0.143 
• R-Value Observed: 0.144 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.249	α = 90
b = 43.326	β = 110.9
c = 45.744	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Jenson, J.M., Grant, R.A., Keating, A.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-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