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- PDB-2l5b: Solution structure of the transmembrane domain of Bcl-2 member Ha... -

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Basic information

Entry
Database: PDB / ID: 2l5b
TitleSolution structure of the transmembrane domain of Bcl-2 member Harakiri in micelles
ComponentsActivator of apoptosis harakiri
KeywordsAPOPTOSIS / Bcl-2 / BH3-only / Harakiri / transmembrane domain
Function / homology
Function and homology information


positive regulation of release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / positive regulation of apoptotic process / apoptotic process / mitochondrion / membrane
Similarity search - Function
Activator of apoptosis harakiri / Activator of apoptosis harakiri / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature.
Similarity search - Domain/homology
Activator of apoptosis harakiri
Similarity search - Component
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsBarrera-Vilarmau, S. / Obregon, P. / de Alba, E.
CitationJournal: Plos One / Year: 2011
Title: Intrinsic order and disorder in the bcl-2 member harakiri: insights into its proapoptotic activity.
Authors: Barrera-Vilarmau, S. / Obregon, P. / de Alba, E.
History
DepositionOct 29, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Activator of apoptosis harakiri


Theoretical massNumber of molelcules
Total (without water)3,3221
Polymers3,3221
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Activator of apoptosis harakiri / BH3-interacting domain-containing protein 3 / Neuronal death protein DP5


Mass: 3321.918 Da / Num. of mol.: 1 / Fragment: UNP Residues 61-91 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: O00198

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-13C HSQC
1412D 1H-1H COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0-1.5 mM Hrk-TM, 200 mM D25 SDS, 5 mM D15 TCEP, 0.1 mM sodium azide, 35% v/v D3 methanol, 95% H2O/5% D2O95% H2O/5% D2O
21.0-1.5 mM Hrk-TM, 200 mM D25 SDS, 0.1 mM sodium azide, 5 mM D15 TCEP, 35% v/v D4 methanol, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMHrk-TM-11.0-1.51
200 mMSDS-2D251
5 mMTCEP-3D151
0.1 mMsodium azide-41
35 v/vmethanol-5D31
mMHrk-TM-61.0-1.52
200 mMSDS-7D252
0.1 mMsodium azide-82
5 mMTCEP-9D152
35 v/vmethanol-10D42
Sample conditionsIonic strength: 0.2 / pH: 3.2 / Pressure: ambient / Temperature: 323 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TOPSPINBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
SPARKYGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR_NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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