2J5D

NMR structure of BNIP3 transmembrane domain in lipid bicelles

Summary for 2J5D

• Entry DOI: 10.2210/pdb2j5d/pdb
• NMR Information: BMRB: 7288
• Descriptor: BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3 (1 entity in total)
• Functional Keywords: membrane protein, mitochondrion, transmembrane, transmembrane domain, bcl-2, bnip3, membrane, homodimer, apoptosis
• Biological source: HOMO SAPIENS (HUMAN)
• Total number of polymer chains: 2
• Total formula weight: 9853.87

Authors

Bocharov, E.V.,Pustovalova, Y.E.,Volynsky, P.E.,Maslennikov, I.V.,Goncharuk, M.V.,Ermolyuk, Y.S.,Arseniev, A.S. (deposition date: 2006-09-14, release date: 2007-04-17, Last modification date: 2024-05-15)

Primary citation

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.
Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger.
J. Biol. Chem., 282:16256-16266, 2007

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 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.

PubMed: 17412696
DOI: 10.1074/jbc.M701745200

Experimental method

SOLUTION NMR