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- PDB-1f16: SOLUTION STRUCTURE OF A PRO-APOPTOTIC PROTEIN BAX -

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Entry
Database: PDB / ID: 1f16
TitleSOLUTION STRUCTURE OF A PRO-APOPTOTIC PROTEIN BAX
ComponentsPROTEIN (APOPTOSIS REGULATOR BAX, MEMBRANE ISOFORM ALPHA)
KeywordsAPOPTOSIS / HELICAL PROTEIN
Function / homology
Function and homology information


release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process ...release of matrix enzymes from mitochondria / BAX complex / B cell receptor apoptotic signaling pathway / Activation, translocation and oligomerization of BAX / B cell apoptotic process / positive regulation of apoptotic DNA fragmentation / NTRK3 as a dependence receptor / BAK complex / mitochondrial permeability transition pore complex / mitochondrial fragmentation involved in apoptotic process / Release of apoptotic factors from the mitochondria / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / endoplasmic reticulum calcium ion homeostasis / mitochondrial fusion / apoptotic mitochondrial changes / execution phase of apoptosis / Bcl-2 family protein complex / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of IRE1-mediated unfolded protein response / pore complex / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / cellular response to unfolded protein / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein binding / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of mitochondrial membrane potential / Hsp70 protein binding / apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to virus / positive regulation of protein-containing complex assembly / response to toxic substance / positive regulation of neuron apoptotic process / nuclear envelope / channel activity / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions ...Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsSuzuki, M. / Youle, R.J. / Tjandra, N.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of Bax: coregulation of dimer formation and intracellular localization.
Authors: Suzuki, M. / Youle, R.J. / Tjandra, N.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: PROTEIN (APOPTOSIS REGULATOR BAX, MEMBRANE ISOFORM ALPHA)


Theoretical massNumber of molelcules
Total (without water)21,2041
Polymers21,2041
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 / 50structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein PROTEIN (APOPTOSIS REGULATOR BAX, MEMBRANE ISOFORM ALPHA)


Mass: 21204.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-SEPARATED NOESY
1214D 13C-SEPARATED NOESY
1313D 15N-SEPARATED NOESY
NMR detailsText: STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY. EXPERIMENTAL DIPOLAR COUPLING RESTRAINTS WERE USED IN STRUCTURE DETERMINATION.

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Sample preparation

DetailsContents: 1MM BAX U-15N,13C; 10mM TRIS-ACETATE PH 6.0 2MM DTT
Sample conditionsIonic strength: 10 mM / pH: 6 / Pressure: AMBIENT / Temperature: 305.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.84BRUNGERrefinement
NMRPIPE 1.7 REV1999.039.11.31structure solution
PIPP4.1.5structure solution
UXNMR2.5structure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING, MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURE WAS BASED ON 2426 NOE RESTRAINTS, 123 DIHEDRAL, 178 HYDROGEN BONDS, 575 DIPOLAR COUPLING RESTRAINTS.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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