Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.43 kDa 
• Atom Count: 1453 
• Modelled Residue Count: 163 
• Deposited Residue Count: 171 
• Unique protein chains: 1

2IMS

The X-ray Structure of a Bak Homodimer Reveals an Inhibitory Zinc Binding Site

• PDB DOI: 10.2210/pdb2IMS/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-04 Released: 2006-12-26 
• Deposition Author(s): Moldoveanu, T., Liu, Q., Tocilj, A., Watson, M., Shore, G.C., Gehring, K.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

The X-Ray Structure of a BAK Homodimer Reveals an Inhibitory Zinc Binding Site

Moldoveanu, T., Liu, Q., Tocilj, A., Watson, M., Shore, G., Gehring, K.

(2006) Mol Cell 24: 677-688

• PubMed: 17157251 
• DOI: 10.1016/j.molcel.2006.10.014
• Primary Citation of Related Structures:  
  2IMS, 2IMT


• PubMed Abstract: 
  

BAK/BAX-mediated mitochondrial outer-membrane permeabilization (MOMP) drives cell death during development and tissue homeostasis from zebrafish to humans. In most cancers, this pathway is inhibited by BCL-2 family antiapoptotic members, which bind and block the action of proapoptotic BCL proteins. We report the 1.5 A crystal structure of calpain-proteolysed BAK, cBAK, to reveal a zinc binding site that regulates its activity via homodimerization. cBAK contains an occluded BH3 peptide binding pocket that binds a BID BH3 peptide only weakly . Nonetheless, cBAK requires activation by truncated BID to induce cytochrome c release in mitochondria isolated from bak/bax double-knockout mouse embryonic fibroblasts. The BAK-mediated MOMP is inhibited by low micromolar zinc levels. This inhibition is alleviated by mutation of the zinc-coordination site in BAK. Our results link directly the antiapoptotic effects of zinc to BAK.

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Organizational Affiliation: 

Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, Canada H3G 1Y6. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator BAK	A	171	Homo sapiens	Mutation(s): 4  Gene Names: BAK1, BAK, BCL2L7, CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16611 (Homo sapiens) Explore Q16611  Go to UniProtKB:  Q16611
PHAROS:  Q16611 GTEx:  ENSG00000030110

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.527	α = 90
b = 53.662	β = 115.05
c = 58.281	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-04 
• Released Date: 2006-12-26 
Deposition Author(s): Moldoveanu, T., Liu, Q., Tocilj, A., Watson, M., Shore, G.C., Gehring, K.B.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description