Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 197.96 kDa 
• Atom Count: 14198 
• Modelled Residue Count: 1760 
• Deposited Residue Count: 1784 
• Unique protein chains: 3

2G5B

Crystal Structure of the anti-Bax monoclonal antibody 6A7 and a Bax peptide.

• PDB DOI: 10.2210/pdb2G5B/pdb

• Classification: APOPTOSIS
• Organism(s): Mus musculus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2006-02-22 Released: 2006-07-25 
• Deposition Author(s): Peyerl, F.W., Dai, S., Murphy, G.A., Marrack, P., Kappler, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.275 
• R-Value Work: 0.234 

Literature

Elucidation of some Bax conformational changes through crystallization of an antibody-peptide complex.

Peyerl, F.W., Dai, S., Murphy, G.A., Crawford, F., White, J., Marrack, P., Kappler, J.W.

(2007) Cell Death Differ 14: 447-452

• PubMed: 16946732 
• DOI: 10.1038/sj.cdd.4402025
• Primary Citation of Related Structures:  
  2G5B


• PubMed Abstract: 
  

The Bcl-2 family member Bax plays a critical role in apoptosis. In healthy resting cells, Bax resides in the cytoplasm and loosely attached to the mitochondrial membrane. Apoptotic stimuli induce Bax activation, which is characterized by translocation and multimerization on the mitochondrial membrane surface resulting in exposure of an amino terminal epitope recognized by the monoclonal antibody 6A7. To understand the structural changes that occur during Bax activation, we determined the crystal structure of a Bax peptide bound to the 6A7 Fab fragment to a resolution of 2.3 A. The structure reveals the conformation of the 6A7 peptide epitope on Bax in the activated form and elucidates the extensive structural changes that Bax must undergo during the conversion from its native to its activated conformation.

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Organizational Affiliation: 

1Howard Hughes Medical Institute, Integrated Department of Immunology, Zuckerman Family/Canyon Ranch Crystallography Laboratory, National Jewish Medical and Research Center, Denver, CO 80206, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6A7 Fab Light Chain	A, C, E, G	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6A7 Fab Heavy Chain	B, D, F, H	222	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P84751 (Mus musculus) Explore P84751  Go to UniProtKB:  P84751

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bax Peptide	I, J, K, L	7	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q07812 (Homo sapiens) Explore Q07812  Go to UniProtKB:  Q07812
PHAROS:  Q07812 GTEx:  ENSG00000087088

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Entity ID: 6
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	Q [auth A], R [auth A], S [auth C], T [auth C], U [auth E], V [auth E], W [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.275 
• R-Value Work: 0.234 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.528	α = 90
b = 183.897	β = 90
c = 67.081	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-22 
• Released Date: 2006-07-25 
Deposition Author(s): Peyerl, F.W., Dai, S., Murphy, G.A., Marrack, P., Kappler, J.W.

Revision History  

• Version 1.0: 2006-07-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary