Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.85 kDa 
• Atom Count: 694 
• Modelled Residue Count: 90 
• Deposited Residue Count: 90 
• Unique protein chains: 1

2J5D

NMR structure of BNIP3 transmembrane domain in lipid bicelles

• PDB DOI: 10.2210/pdb2J5D/pdb
• BMRB: 7288

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMMemProtMD


• Deposited: 2006-09-14 Released: 2007-04-17 
• Deposition Author(s): Bocharov, E.V., Pustovalova, Y.E., Volynsky, P.E., Maslennikov, I.V., Goncharuk, M.V., Ermolyuk, Y.S., Arseniev, A.S.

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Experimental Data Snapshot

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

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

• PubMed: 17412696 
• DOI: 10.1074/jbc.M701745200
• Primary Citation of Related Structures:  
  2J5D


• 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.

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Organizational Affiliation: 

Laboratory of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow 117997, Russia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3	A, B	45	Homo sapiens	Mutation(s): 0  Gene Names: BNIP3, NIP3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q12983 (Homo sapiens) Explore Q12983  Go to UniProtKB:  Q12983
PHAROS:  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

Entry History 

Deposition Data

• Deposited Date: 2006-09-14 
• Released Date: 2007-04-17 
Deposition Author(s): Bocharov, E.V., Pustovalova, Y.E., Volynsky, P.E., Maslennikov, I.V., Goncharuk, M.V., Ermolyuk, Y.S., Arseniev, A.S.

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Database references, Source and taxonomy
• Version 1.4: 2020-01-15
  Changes: Other