5UUM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.346 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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, Massachusetts Institute of Technology, Cambridge, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B
156Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bfl-1 specific peptide FS2
C, D
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C, D
NON-POLYMERH2 N

--

ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.346 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 132.617α = 90.00
b = 62.760β = 98.14
c = 48.788γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM110048

Revision History 

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