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Apoptosis PDB id
1zy3
Jmol
Contents
Protein chains
170 a.a. *
20 a.a. *
* Residue conservation analysis
PDB id:
1zy3
Name: Apoptosis
Title: Structural model of complex of bcl-w protein with bid bh3- peptide
Structure: Apoptosis regulator bcl-w. Chain: a. Fragment: residues 2-171. Synonym: bcl-2-like 2 protein. Engineered: yes. Mutation: yes. Bh3-peptide from bh3 interacting domain death agonist protein. Chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 10 models
Authors: A.Y.Denisov,K.Gehring
Key ref:
A.Y.Denisov et al. (2006). Structural Model of the BCL-w-BID Peptide Complex and Its Interactions with Phospholipid Micelles(,). Biochemistry, 45, 2250-2256. PubMed id: 16475813 DOI: 10.1021/bi052332s
Date:
09-Jun-05     Release date:   14-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q92843  (B2CL2_HUMAN) -  Bcl-2-like protein 2
Seq:
Struc: 		193 a.a.
170 a.a.*
Protein chain
Pfam   ArchSchema ?
P55957  (BID_HUMAN) -  BH3-interacting domain death agonist
Seq:
Struc: 		195 a.a.
20 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     regulation of apoptosis   2 terms 

 

 
DOI no: 10.1021/bi052332s Biochemistry 45:2250-2256 (2006)
PubMed id: 16475813  
 
 
Structural Model of the BCL-w-BID Peptide Complex and Its Interactions with Phospholipid Micelles(,).
A.Y.Denisov, G.Chen, T.Sprules, T.Moldoveanu, P.Beauparlant, K.Gehring.
 
  ABSTRACT  
 
A peptide corresponding to the BH3 region of the proapoptotic protein, BID, could be bound in the cleft of the antiapoptotic protein, BCL-w. This binding induced major conformational rearrangements in both the peptide and protein components of the complex and led to the displacement and unfolding of the BCL-w C-terminal alpha-helix. The structure of BCL-w with a bound BID-BH3 peptide was determined using NMR spectroscopy and molecular docking. These studies confirmed that a region of 16 residues of the BID-BH3 peptide is responsible for its strong binding to BCL-w and BCL-x(L). The interactions of BCL-w and the BID-BH3 peptide complex with dodecylphosphocholine micelles were characterized and showed that the conformational change of BCL-w upon lipid binding occurred at the same time as the release and unfolding of the BH3 peptide.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20066663 E.Fire, S.V.Gullá, R.A.Grant, and A.E.Keating (2010).
Mcl-1-Bim complexes accommodate surprising point mutations via minor structural changes.
  Protein Sci, 19, 507-519.
PDB codes: 3kj0 3kj1 3kj2
20008353 S.Bleicken, M.Classen, P.V.Padmavathi, T.Ishikawa, K.Zeth, H.J.Steinhoff, and E.Bordignon (2010).
Molecular details of Bax activation, oligomerization, and membrane insertion.
  J Biol Chem, 285, 6636-6647.  
19293158 G.Moroy, E.Martin, A.Dejaegere, and R.H.Stote (2009).
Molecular basis for Bcl-2 homology 3 domain recognition in the Bcl-2 protein family: identification of conserved hot spot interactions.
  J Biol Chem, 284, 17499-17511.  
19766123 J.Sun, D.M.Abdeljabbar, N.Clarke, M.L.Bellows, C.A.Floudas, and A.J.Link (2009).
Reconstitution and engineering of apoptotic protein interactions on the bacterial cell surface.
  J Mol Biol, 394, 297-305.  
19640296 W.J.Mo, X.P.Fu, X.T.Han, G.Y.Yang, J.G.Zhang, F.H.Guo, Y.Huang, Y.M.Mao, Y.Li, and Y.Xie (2009).
A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression.
  BMC Genomics, 10, 340.  
19670908 Y.Yao, A.A.Bobkov, L.A.Plesniak, and F.M.Marassi (2009).
Mapping the interaction of pro-apoptotic tBID with pro-survival BCL-XL.
  Biochemistry, 48, 8704-8711.  
18665234 B.Köhler, S.Anguissola, C.G.Concannon, M.Rehm, D.Kögel, and J.H.Prehn (2008).
Bid participates in genotoxic drug-induced apoptosis of HeLa cells and is essential for death receptor ligands' apoptotic and synergistic effects.
  PLoS ONE, 3, e2844.  
19641503 E.Lomonosova, and G.Chinnadurai (2008).
BH3-only proteins in apoptosis and beyond: an overview.
  Oncogene, 27, S2-19.  
18195012 O.Terrones, A.Etxebarria, A.Landajuela, O.Landeta, B.Antonsson, and G.Basañez (2008).
BIM and tBID are not mechanistically equivalent when assisting BAX to permeabilize bilayer membranes.
  J Biol Chem, 283, 7790-7803.  
16645638 M.G.Hinds, C.Smits, R.Fredericks-Short, J.M.Risk, M.Bailey, D.C.Huang, and C.L.Day (2007).
Bim, Bad and Bmf: intrinsically unstructured BH3-only proteins that undergo a localized conformational change upon binding to prosurvival Bcl-2 targets.
  Cell Death Differ, 14, 128-136.  
17597151 X.Fu, J.R.Apgar, and A.E.Keating (2007).
Modeling backbone flexibility to achieve sequence diversity: the design of novel alpha-helical ligands for Bcl-xL.
  J Mol Biol, 371, 1099-1117.  
16763614 L.D.Walensky (2006).
BCL-2 in the crosshairs: tipping the balance of life and death.
  Cell Death Differ, 13, 1339-1350.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.