1R2I

Human Bcl-XL containing a Phe to Leu mutation at position 146

• PDB DOI: https://doi.org/10.2210/pdb1R2I/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-09-26 Released: 2004-02-03 
• Deposition Author(s): O'Neill, J.W., Manion, M.K., Giedt, C.D., Kim, K.M., Zhang, K.Y., Hockenbery, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Bcl-XL mutations suppress cellular sensitivity to antimycin A.

Manion, M.K., O'Neill, J.W., Giedt, C.D., Kim, K.M., Zhang, K.Y., Hockenbery, D.M.

(2004) J Biol Chem 279: 2159-2165

• PubMed: 14534311 
• DOI: https://doi.org/10.1074/jbc.M306021200
• Primary Citation of Related Structures:  
  1R2D, 1R2E, 1R2G, 1R2H, 1R2I


• PubMed Abstract: 
  

  Cells expressing high levels of the BCL-X(L) anti-apoptotic protein are preferentially killed by the mitochondrial inhibitor antimycin A (AA). Computational modeling predicts a binding site for AA in the extended hydrophobic groove on BCL-X(L), previously identified as an interface for dimerization to BAX and related proapoptotic proteins. Here, we identify BCL-X(L) hydrophobic groove mutants with normal cellular anti-apoptotic function but suppressed sensitivity to AA. The LD(50) of AA for cells expressing BCL-X(L) mutants directly correlates with the measured in vitro dissociation constants for AA binding. These results indicate that BCL-X(L) is a principal target mediating AA cytotoxicity.

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Organizational Affiliation: 

Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.57 kDa 
• Atom Count: 1,357 
• Modelled Residue Count: 143 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-X	A	218	Homo sapiens	Mutation(s): 1  Gene Names: BCL-XL
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens) Explore Q07817  Go to UniProtKB:  Q07817
PHAROS:  Q07817 GTEx:  ENSG00000171552

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.187	α = 90
b = 63.187	β = 90
c = 109.874	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-03 
Deposition Author(s): O'Neill, J.W., Manion, M.K., Giedt, C.D., Kim, K.M., Zhang, K.Y., Hockenbery, D.M.

Revision History  

• Version 1.0: 2004-02-03
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-27
  Changes: Database references
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description