4U2V

Bak BH3-in-Groove dimer (GFP)

• PDB DOI:  https://doi.org/10.2210/pdb4U2V/pdb

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


• Deposited: 2014-07-18 Released: 2014-09-10 
• Deposition Author(s): Brouwer, J.M., Colman, P.M., Czabotar, P.E.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Bak Core and Latch Domains Separate during Activation, and Freed Core Domains Form Symmetric Homodimers.

Brouwer, J.M., Westphal, D., Dewson, G., Robin, A.Y., Uren, R.T., Bartolo, R., Thompson, G.V., Colman, P.M., Kluck, R.M., Czabotar, P.E.

(2014) Mol Cell 55: 938-946

• PubMed: 25175025 
• DOI: https://doi.org/10.1016/j.molcel.2014.07.016
• Primary Citation of Related Structures:  
  4U2U, 4U2V


• PubMed Abstract: 
  

Apoptotic stimuli activate and oligomerize the proapoptotic proteins Bak and Bax, resulting in mitochondrial outer-membrane permeabilization and subsequent cell death. This activation can occur when certain BH3-only proteins interact directly with Bak and Bax. Recently published crystal structures reveal that Bax separates into core and latch domains in response to BH3 peptides. The distinguishing characteristics of BH3 peptides capable of directly activating Bax were also elucidated. Here we identify specific BH3 peptides capable of "unlatching" Bak and describe structural insights into Bak activation and oligomerization. Crystal structures and crosslinking experiments demonstrate that Bak undergoes a conformational change similar to that of Bax upon activation. A structure of the Bak core domain dimer provides a high-resolution image of this key intermediate in the pore-forming oligomer. Our results confirm an analogous mechanism for activation and dimerization of Bak and Bax in response to certain BH3 peptides.

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Organizational Affiliation: 

Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142.74 kDa 
• Atom Count: 10,072 
• Modelled Residue Count: 1,227 
• Deposited Residue Count: 1,252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Bcl-2 homologous antagonist/killer	A [auth B], B [auth D], C, D [auth A]	313	Aequorea victoria, Homo sapiens This entity is chimeric	Mutation(s): 3  Gene Names: GFP, BAK1, BAK, BCL2L7, CDN1
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212
Find proteins for Q16611 (Homo sapiens) Explore Q16611  Go to UniProtKB:  Q16611
PHAROS:  Q16611
UniProt Groups	P42212Q16611

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	E [auth B], F [auth D], G [auth D], H [auth D], J [auth A], K [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
MPD	I [auth C], L [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A [auth B], B [auth D], C, D [auth A]	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.19	α = 90
b = 63.84	β = 98.35
c = 122.02	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Brouwer, J.M., Colman, P.M., Czabotar, P.E.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1059331
National Health and Medical Research Council (NHMRC, Australia)	Australia	1023055
National Health and Medical Research Council (NHMRC, Australia)	Australia	1016701

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.3: 2020-01-08
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description