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- PDB-2j5d: NMR structure of BNIP3 transmembrane domain in lipid bicelles -

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Basic information

Entry
Database: PDB / ID: 2j5d
TitleNMR structure of BNIP3 transmembrane domain in lipid bicelles
ComponentsBCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3
KeywordsMEMBRANE PROTEIN / MITOCHONDRION / TRANSMEMBRANE / TRANSMEMBRANE DOMAIN / BCL-2 / BNIP3 / MEMBRANE / HOMODIMER / APOPTOSIS
Function / homology
Function and homology information


mitochondrial protein catabolic process / negative regulation of membrane potential / negative regulation of mitochondrial membrane permeability involved in apoptotic process / granzyme-mediated programmed cell death signaling pathway / cellular response to cobalt ion / autophagic cell death / mitochondrial outer membrane permeabilization / response to oxygen-glucose deprivation / positive regulation of mitochondrial calcium ion concentration / negative regulation of mitochondrial fusion ...mitochondrial protein catabolic process / negative regulation of membrane potential / negative regulation of mitochondrial membrane permeability involved in apoptotic process / granzyme-mediated programmed cell death signaling pathway / cellular response to cobalt ion / autophagic cell death / mitochondrial outer membrane permeabilization / response to oxygen-glucose deprivation / positive regulation of mitochondrial calcium ion concentration / negative regulation of mitochondrial fusion / positive regulation of autophagy of mitochondrion / mitochondrial fragmentation involved in apoptotic process / autophagy of mitochondrion / positive regulation of protein-containing complex disassembly / positive regulation of programmed cell death / negative regulation of programmed cell death / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of mitochondrial membrane permeability / positive regulation of mitochondrial fission / regulation of aerobic respiration / positive regulation of cardiac muscle cell apoptotic process / oligodendrocyte differentiation / negative regulation of mitochondrial membrane potential / positive regulation of release of cytochrome c from mitochondria / positive regulation of macroautophagy / response to axon injury / negative regulation of reactive oxygen species metabolic process / response to hyperoxia / positive regulation of autophagy / brown fat cell differentiation / cardiac muscle cell apoptotic process / reactive oxygen species metabolic process / mitochondrial membrane / response to bacterium / cerebral cortex development / cellular response to hydrogen peroxide / cellular response to mechanical stimulus / GTPase binding / nuclear envelope / cellular response to hypoxia / neuron apoptotic process / defense response to virus / mitochondrial outer membrane / postsynaptic density / response to hypoxia / positive regulation of apoptotic process / dendrite / negative regulation of apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1020 / BNIP3 / BNIP3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
BCL2/adenovirus E1B 19 kDa protein-interacting protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / TAD
AuthorsBocharov, E.V. / Pustovalova, Y.E. / Volynsky, P.E. / Maslennikov, I.V. / Goncharuk, M.V. / Ermolyuk, Y.S. / Arseniev, A.S.
CitationJournal: J. Biol. Chem. / Year: 2007
Title: Unique dimeric structure of BNip3 transmembrane domain suggests membrane permeabilization as a cell death trigger.
Authors: 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.
History
DepositionSep 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 15, 2020Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3
B: BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)9,8542
Polymers9,8542
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 200THE BEST TARGET FUNCTION
Representative

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Components

#1: Protein/peptide BCL2/ADENOVIRUS E1B 19 KDA PROTEIN-INTERACTING PROTEIN 3 / BNIP3 TM


Mass: 4926.933 Da / Num. of mol.: 2
Fragment: HOMODIMERIC TRANSMEMBRANE DOMAIN, RESIDUES 146-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MITOCHONDIONAL PROTEIN FROM BCL-2 FAMILY / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q12983
Sequence detailsWE STUDIED BNIP3 FRAGMENT ARG146-SER190 WHICH CONTAINS THE TRANSMEMBRANE SEGMENT WITH ADJACENT REGION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
1213D-15N-EDITED- NOESY
1313D-15N-EDITED-TOCSY
14113C-HSQC
1513D-13C-EDITED- NOESY
1613D (H)CCH-TOCSY
1712D- NOESY
1812D-TOCSY
1912D-ROESY
1101HNCA
1111HN(CO)CA
1121HN(CA)CB
1131CBCA(CO)NH
1141HBHA(CO)NH
11512D-15N- 13C-F1-FILT.-F3-SEPAR.- NOESY-HSQC
11613D-13C-F1-FILT. -F3-SEPAR.-NOESY-HSQC
NMR detailsText: THE FIRST 12 AND THE LAST 4 STRUCTERES DIFFER IN HIS173 TAUTOMERIC FORM WITH PROTONATED NE OR ND, RESPECTIVELY.

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Sample preparation

DetailsContents: 95% H2O/ 5% D2O
Sample conditionsIonic strength: 20 mM / pH: 5.1 / Pressure: 1.0 atm / Temperature: 313.0 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
GROMACSLINDAHLrefinement
CYANAstructure solution
RefinementMethod: TAD / Software ordinal: 1
Details: NMR-DERIVED STRUCTURES OF BNIP3 TM DIMERIC WERE RELAXATED BY MOLECULAR DYNAMICS IN EXPLICIT LIPID DMPC BILAYER USING NMR CONSTRAINTS THERE ARE SLOW CONFORMATIONAL EXCHANGE IN HYDROGEN BOND ...Details: NMR-DERIVED STRUCTURES OF BNIP3 TM DIMERIC WERE RELAXATED BY MOLECULAR DYNAMICS IN EXPLICIT LIPID DMPC BILAYER USING NMR CONSTRAINTS THERE ARE SLOW CONFORMATIONAL EXCHANGE IN HYDROGEN BOND NET OF (SER172, HIS173)2 CLUSTER ON THE DIMERIZATION INTERFACE.
NMR ensembleConformer selection criteria: THE BEST TARGET FUNCTION / Conformers calculated total number: 200 / Conformers submitted total number: 16

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