3IIH | pdb_00003iih

Crystal structure of mouse Bcl-xl (wt) at pH 6.0

• PDB DOI: https://doi.org/10.2210/pdb3IIH/pdb

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


• Deposited: 2009-08-01 Released: 2010-04-14 
• Deposition Author(s): Priyadarshi, A., Hwang, K.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural insights into mouse anti-apoptotic Bcl-xl reveal affinity for Beclin 1 and gossypol.

Priyadarshi, A., Roy, A., Kim, K.S., Kim, E.E., Hwang, K.Y.

(2010) Biochem Biophys Res Commun 394: 515-521

• PubMed: 20206602 
• DOI: https://doi.org/10.1016/j.bbrc.2010.03.002
• Primary Citation Related Structures: 
  3IHC, 3IHD, 3IHE, 3IHF, 3IIG, 3IIH, 3ILB, 3ILC


• PubMed Abstract: 
  

  This study reports the crystal structures of Bcl-xl wild type and three Bcl-xl mutants (Y101A, F105A, and R139A) with amino acid substitutions in the hydrophobic groove of the Bcl-xl BH3 domain. An additional 12 ordered residues were observed in a highly flexible loop between the alpha1 and alpha2 helices, and were recognized as an important deamidation site for the regulation of apoptosis. The autophagy-effector protein, Beclin 1, contains a novel BH3 domain (residues 101-125), which binds to the surface cleft of Bcl-xl, as confirmed by nuclear magnetic resonance (NMR) spectroscopy and analytical gel-filtration results. Gossypol, a potent inhibitor of Bcl-xl, had a K(d) value of 0.9 microM. In addition, the structural and biochemical analysis of five Bcl-xl substitution mutants will provide structural insights into the design and development of anti-cancer drugs.

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Organizational Affiliation: 
• Biomedical Research Center, KIST, Republic of Korea.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.06 kDa 
• Atom Count: 1,154 
• Modeled Residue Count: 142 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bcl-2-like protein 1	A	196	Mus musculus	Mutation(s): 0  Gene Names: Bcl-xl, Bcl2l, Bcl2l1, Bclx
UniProt
Find proteins for Q64373 (Mus musculus) Explore Q64373  Go to UniProtKB:  Q64373

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.169	α = 90
b = 63.169	β = 90
c = 110.352	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Priyadarshi, A., Hwang, K.Y.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-11-20
  Changes: Database references
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description