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- PDB-2ka2: Solution NMR structure of BNIP3 transmembrane peptide dimer in de... -

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Entry
Database: PDB / ID: 2ka2
TitleSolution NMR structure of BNIP3 transmembrane peptide dimer in detergent micelles with His173-Ser172 intermonomer hydrogen bond restraints
ComponentsBCL2/adenovirus E1B 19 kDa protein-interacting protein 3
KeywordsMEMBRANE PROTEIN / integral membrane protein / membrane helix-helix interactions / bnip3 / transmembrane domain / homodimer / membrane protein folding / Apoptosis / Host-virus interaction / Mitochondrion / Phosphoprotein
Function / homology
Function and homology information


negative regulation of membrane potential / mitochondrion autophagosome adaptor activity / negative regulation of mitochondrial membrane permeability involved in apoptotic process / endoplasmic reticulum-autophagosome adaptor activity / cellular response to cobalt ion / granzyme-mediated programmed cell death signaling pathway / mitochondrial outer membrane permeabilization / response to oxygen-glucose deprivation / positive regulation of mitochondrial calcium ion concentration / autophagic cell death ...negative regulation of membrane potential / mitochondrion autophagosome adaptor activity / negative regulation of mitochondrial membrane permeability involved in apoptotic process / endoplasmic reticulum-autophagosome adaptor activity / cellular response to cobalt ion / granzyme-mediated programmed cell death signaling pathway / mitochondrial outer membrane permeabilization / response to oxygen-glucose deprivation / positive regulation of mitochondrial calcium ion concentration / autophagic cell death / negative regulation of mitochondrial fusion / positive regulation of autophagy of mitochondrion / mitochondrial fragmentation involved in apoptotic process / mitochondrial protein catabolic process / positive regulation of protein-containing complex disassembly / positive regulation of programmed cell death / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of mitochondrial membrane permeability / negative regulation of programmed cell death / reticulophagy / autophagy of mitochondrion / regulation of aerobic respiration / positive regulation of mitochondrial fission / positive regulation of release of cytochrome c from mitochondria / oligodendrocyte differentiation / negative regulation of mitochondrial membrane potential / positive regulation of macroautophagy / mitophagy / negative regulation of reactive oxygen species metabolic process / response to axon injury / response to hyperoxia / brown fat cell differentiation / positive regulation of cardiac muscle cell apoptotic process / cardiac muscle cell apoptotic process / positive regulation of autophagy / reactive oxygen species metabolic process / response to bacterium / mitochondrial membrane / cerebral cortex development / cellular response to hydrogen peroxide / cellular response to mechanical stimulus / nuclear envelope / GTPase binding / cellular response to hypoxia / neuron apoptotic process / defense response to virus / mitochondrial outer membrane / response to hypoxia / postsynaptic density / positive regulation of apoptotic process / dendrite / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
BCL2/adenovirus E1B 19 kDa protein-interacting protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSulistijo, E.S. / MacKenzie, K.R.
CitationJournal: Biochemistry / Year: 2009
Title: Structural basis for dimerization of the BNIP3 transmembrane domain
Authors: Sulistijo, E.S. / Mackenzie, K.R.
History
DepositionOct 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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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)7,5812
Polymers7,5812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide BCL2/adenovirus E1B 19 kDa protein-interacting protein 3


Mass: 3790.588 Da / Num. of mol.: 2 / Fragment: transmembrane domain, residues 154-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BNIP3, NIP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12983

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CN-NOESY-HSQC
1213D 15N-edited NOESY-HSQC
1313D 13C-edited NOESY-HSQC optimized for aromatic carbon
141half-filtered 3D CN-NOESY-HSQC
1512D spin-echo difference CT HSQC
161HNHA
171HNCA
181CBCACONNH
191HNCO
1101H(C)CH-COSY
1111(H)CCH-TOCSY
1121(HB)CB(CGCD)HD
1131(HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 0.4 mM [U-100% 13C; U-100% 15N] Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3, 0.6 mM Bcl2/Adenovirus E1B 19 kDa protein-interacting protein 3, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMBcl2/Adenovirus E1B 19 kDa protein-interacting protein 3-1[U-100% 13C; U-100% 15N]1
0.6 mMBcl2/Adenovirus E1B 19 kDa protein-interacting protein 3-21
Sample conditionspH: 5.1 / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Inferred intermonomer hydrogen bond restraints between His173-Ser172 are included in calculation. Intermonomer hydrogen bond restraints between His173-Ser172 are included. THE CALCULATION OF ...Details: Inferred intermonomer hydrogen bond restraints between His173-Ser172 are included in calculation. Intermonomer hydrogen bond restraints between His173-Ser172 are included. THE CALCULATION OF THIS STRUCTURE INCLUDES 2 ADDITIONAL HYDROGEN BOND RESTRAINTS THAT WERE DERIVED FROM MUTAGENESIS DATA.
NMR constraintsNOE constraints total: 2036 / NOE intraresidue total count: 1244 / NOE long range total count: 108 / NOE medium range total count: 226 / NOE sequential total count: 386 / Hydrogen bond constraints total count: 58 / Protein chi angle constraints total count: 22 / Protein other angle constraints total count: 8 / Protein phi angle constraints total count: 34 / Protein psi angle constraints total count: 34
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 50 / Conformers submitted total number: 20

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