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- PDB-2kua: Solution structure of a divergent Bcl-2 protein -

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Basic information

Entry
Database: PDB / ID: 2kua
TitleSolution structure of a divergent Bcl-2 protein
ComponentsBcl-2-like protein 10
KeywordsAPOPTOSIS / Boo / Diva / Bcl-2 / BH3-only / Membrane / Mitochondrion / Nucleus / Transmembrane
Function / homology
Function and homology information


mitochondria-associated endoplasmic reticulum membrane contact site / caspase binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear membrane / mitochondrial outer membrane / membrane => GO:0016020 / positive regulation of apoptotic process ...mitochondria-associated endoplasmic reticulum membrane contact site / caspase binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to DNA damage / nuclear membrane / mitochondrial outer membrane / membrane => GO:0016020 / positive regulation of apoptotic process / protein heterodimerization activity / apoptotic process / negative regulation of apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / cytosol
Similarity search - Function
Blc2-like / Apoptosis Regulator Bcl-x / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsRautureau, G.J. / Day, C.L. / Hinds, M.G.
CitationJournal: Proteins / Year: 2010
Title: The structure of Boo/Diva reveals a divergent Bcl-2 protein.
Authors: Rautureau, G.J. / Day, C.L. / Hinds, M.G.
History
DepositionFeb 16, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 10


Theoretical massNumber of molelcules
Total (without water)19,5071
Polymers19,5071
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 / 600structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Bcl-2-like protein 10 / Bcl2-L-10 / Apoptosis regulator Bcl-B / Anti-apoptotic protein Boo / Bcl-2 homolog Diva


Mass: 19507.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Boo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z0F3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCA
1613D HN(CO)CA
1713D 1H-15N NOESY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
11013D H(CCO)NH

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Sample preparation

DetailsContents: 50mM sodium phosphate-1, 50mM sodium chloride-2, 1.5mM [U-95% 13C; U-95% 15N] Bcl-2-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
50 mMsodium chloride-21
1.5 mMBcl-2-3[U-95% 13C; U-95% 15N]1
Sample conditionspH: 6.7 / Pressure: ambient / Temperature: 303.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: CYANA 2.1
NMR constraintsNOE constraints total: 3011 / NOE intraresidue total count: 670 / NOE long range total count: 759 / NOE medium range total count: 730 / NOE sequential total count: 852 / Hydrogen bond constraints total count: 132 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 130 / Protein psi angle constraints total count: 130
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 600 / Conformers submitted total number: 20 / Representative conformer: 1

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