9CPN | pdb_00009cpn

Structural basis of BAK sequestration by MCL-1 and consequences for apoptosis initiation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.243 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CPN

This is version 1.0 of the entry. See complete history

Literature

Structural basis of BAK sequestration by MCL-1 in apoptosis.

Srivastava, S.Sekar, G.Ojoawo, A.Aggarwal, A.Ferreira, E.Uchikawa, E.Yang, M.Grace, C.R.Dey, R.Lin, Y.L.Guibao, C.D.Jayaraman, S.Mukherjee, S.Kossiakoff, A.A.Dong, B.Myasnikov, A.Moldoveanu, T.

(2025) Mol Cell 85: 1606-1623.e10

  • DOI: https://doi.org/10.1016/j.molcel.2025.03.013
  • Primary Citation Related Structures: 
    9CPE, 9CPF, 9CPH, 9CPN

  • PubMed Abstract: 

    Apoptosis controls cell fate, ensuring tissue homeostasis and promoting disease when dysregulated. The rate-limiting step in apoptosis is mitochondrial poration by the effector B cell lymphoma 2 (BCL-2) family proteins BAK and BAX, which are activated by initiator BCL-2 homology 3 (BH3)-only proteins (e.g., BIM) and inhibited by guardian BCL-2 family proteins (e.g., MCL-1). We integrated structural, biochemical, and pharmacological approaches to characterize the human prosurvival MCL-1:BAK complex assembled from their BCL-2 globular core domains. We reveal a canonical interaction with BAK BH3 bound to the hydrophobic groove of MCL-1 and disordered and highly dynamic BAK regions outside the complex interface. We predict similar conformations of activated effectors in complex with other guardians or effectors. The MCL-1:BAK complex is a major cancer drug target. We show that MCL-1 inhibitors are inefficient in neutralizing the MCL-1:BAK complex, requiring high doses to initiate apoptosis. Our study underscores the need to design superior clinical candidate MCL-1 inhibitors.


  • Organizational Affiliation
    • Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.

Macromolecule Content 

  • Total Structure Weight: 240.31 kDa 
  • Atom Count: 17,760 
  • Modeled Residue Count: 2,126 
  • Deposited Residue Count: 2,156 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B, C, D
517synthetic constructMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Bcl-2 homologous antagonist/killer
E, F, G, H
22Homo sapiensMutation(s): 0 
Gene Names: BAK1BAKBCL2L7CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens)
Explore Q16611 
Go to UniProtKB:  Q16611
PHAROS:  Q16611
GTEx:  ENSG00000030110 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16611
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.614α = 90
b = 109.33β = 100.68
c = 125.127γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM129470

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release