2J5D

NMR structure of BNIP3 transmembrane domain in lipid bicelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 16 
  • Selection Criteria: THE BEST TARGET FUNCTION 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger.

Bocharov, E.V.Pustovalova, Y.E.Pavlov, K.V.Volynsky, P.E.Goncharuk, M.V.Ermolyuk, Y.S.Karpunin, D.V.Schulga, A.A.Kirpichnikov, M.P.Efremov, R.G.Maslennikov, I.V.Arseniev, A.S.

(2007) J. Biol. Chem. 282: 16256-16266

  • DOI: 10.1074/jbc.M701745200

  • PubMed Abstract: 
  • BNip3 is a prominent representative of apoptotic Bcl-2 proteins with rather unique properties initiating an atypical programmed cell death pathway resembling both necrosis and apoptosis. Many Bcl-2 family proteins modulate the permeability state of t ...

    BNip3 is a prominent representative of apoptotic Bcl-2 proteins with rather unique properties initiating an atypical programmed cell death pathway resembling both necrosis and apoptosis. Many Bcl-2 family proteins modulate the permeability state of the outer mitochondrial membrane by forming homo- and hetero-oligomers. The structure and dynamics of the homodimeric transmembrane domain of BNip3 were investigated with the aid of solution NMR in lipid bicelles and molecular dynamics energy relaxation in an explicit lipid bilayer. The right-handed parallel helix-helix structure of the domain with a hydrogen bond-rich His-Ser node in the middle of the membrane, accessibility of the node for water, and continuous hydrophilic track across the membrane suggest that the domain can provide an ion-conducting pathway through the membrane. Incorporation of the BNip3 transmembrane domain into an artificial lipid bilayer resulted in pH-dependent conductivity increase. A possible biological implication of the findings in relation to triggering necrosis-like cell death by BNip3 is discussed.


    Organizational Affiliation

    Laboratory of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia. bon@nmr.ru




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3
A, B
45Homo sapiensMutation(s): 0 
Gene Names: BNIP3 (NIP3)
Find proteins for Q12983 (Homo sapiens)
Go to Gene View: BNIP3
Go to UniProtKB:  Q12983
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 16 
  • Selection Criteria: THE BEST TARGET FUNCTION 
  • Olderado: 2J5D Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-28
    Type: Database references, Source and taxonomy