1PQ1 | pdb_00001pq1

Crystal structure of Bcl-xl/Bim

• PDB DOI: https://doi.org/10.2210/pdb1PQ1/pdb

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


• Deposited: 2003-06-17 Released: 2003-09-23 
• Deposition Author(s): Liu, X., Dai, S., Zhu, Y., Marrack, P., Kappler, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

The structure of a Bcl-xl/Bim fragment complex: Implications for Bim function

Liu, X., Dai, S., Zhu, Y., Marrack, P., Kappler, J.W.

(2003) Immunity 19: 341-352

• PubMed: 14499110 
• DOI: https://doi.org/10.1016/s1074-7613(03)00234-6
• Primary Citation Related Structures: 
  1PQ0, 1PQ1


• PubMed Abstract: 
  

  After antigen-driven expansion, the majority of T cells involved in an immune response die rapidly by apoptosis dependent on the Bcl-2 related proteins, Bim and Bax or Bak. The details of how these proteins are activated and interact are still unclear. The crystal structure of mouse Bcl-x(L) bound to a long helical fragment of Bim indicates that the structure of Bim is very different from proteins with a Bcl-2-like fold and may leave the BH3 region of Bim constitutively exposed. Based on the structural homology between Bcl-x(L) and Bax, we predicted that binding of Bim to Bax would require displacement of the Bax penultimate alpha helix. Consistent with this prediction, truncation of this short helix was required for Bim/Bax interaction and led to spontaneous activation of Bax. Our results suggest a way in which both Bim and Bax/Bak might be required for activated T cell apoptosis.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, National Jewish Medical and Research Center, 1400 Jackson Street, Denver, CO 80206, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 26.18 kDa 
• Atom Count: 1,627 
• Modeled Residue Count: 180 
• Deposited Residue Count: 229 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptosis regulator Bcl-X	A	196	Mus musculus	Mutation(s): 0  Gene Names: BCL2L1 OR BCL2L OR BCLX
UniProt
Find proteins for Q64373 (Mus musculus) Explore Q64373  Go to UniProtKB:  Q64373

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL2-like protein 11	B	33	Mus musculus	Mutation(s): 0  Gene Names: BCL2L11 OR BIM
UniProt & NIH Common Fund Data Resources
Find proteins for O54918 (Mus musculus) Explore O54918  Go to UniProtKB:  O54918
IMPC:  MGI:1197519

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.1	α = 90
b = 47.34	β = 110.1
c = 49.28	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-23 
Deposition Author(s): Liu, X., Dai, S., Zhu, Y., Marrack, P., Kappler, J.W.

Revision History  

• Version 1.0: 2003-09-23
  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: 2023-08-16
  Changes: Data collection, Database references, Refinement description