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- PDB-1o0l: THE STRUCTURE OF BCL-W REVEALS A ROLE FOR THE C-TERMINAL RESIDUES... -

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Basic information

Entry
Database: PDB / ID: 1o0l
TitleTHE STRUCTURE OF BCL-W REVEALS A ROLE FOR THE C-TERMINAL RESIDUES IN MODULATING BIOLOGICAL ACTIVITY
ComponentsApoptosis regulator Bcl-W
KeywordsAPOPTOSIS / BCL-2 / HELICAL BUNDLE / BINDING GROOVE / BH3
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / cellular response to glycine / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to estradiol stimulus / response to ischemia ...negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / cellular response to glycine / negative regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to estradiol stimulus / response to ischemia / cellular response to amyloid-beta / intrinsic apoptotic signaling pathway in response to DNA damage / disordered domain specific binding / spermatogenesis / regulation of apoptotic process / mitochondrial outer membrane / protein heterodimerization activity / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-W / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH1 motif, conserved site ...Apoptosis regulator, Bcl-W / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Blc2-like / Apoptosis Regulator Bcl-x / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry torsion angle dynamics simulated annealing
AuthorsHinds, M.G. / Lackmann, M. / Skea, G.L. / Harrison, P.J. / Huang, D.C.S. / Day, C.L.
CitationJournal: Embo J. / Year: 2003
Title: The structure of Bcl-w reveals a role for the C-terminal residues in modulating biological activity
Authors: Hinds, M.G. / Lackmann, M. / Skea, G.L. / Harrison, P.J. / Huang, D.C.S. / Day, C.L.
History
DepositionFeb 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: Apoptosis regulator Bcl-W


Theoretical massNumber of molelcules
Total (without water)20,2551
Polymers20,2551
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Apoptosis regulator Bcl-W / BCL2-like 2 protein


Mass: 20254.684 Da / Num. of mol.: 1 / Mutation: A128E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L2 OR BCLW OR KIAA0271 / Plasmid: pGex6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92843

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2223D 15N-separated NOESY
232HNHA
3433D 13C-separated NOESY
NMR detailsText: The structure was determined using heteronuclear 3D NMR.

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Bcl-w50mM Sodium Phosphate, 70mM NaCl, 2mM TCEP, 95% H2O, 5% D2O
21 mM, U-15N Bcl-w50mM Sodium Phosphate, 70mM NaCl, 2mM TCEP, 95% H2O, 5% D2O
31 mM, U-13C, 15N, Bcl-w50mM Sodium Phosphate, 70mM NaCl, 2mM TCEP, 95% H2O, 5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120mM 6.7 ambient 303.15 K
2120mM 6.7 ambient 303.15 K
3120mM 6.7 ambient 303.15 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Bruker A.G.collection
XEASY1.3Bartels et al. J. Biomol. NMR 1995, 6, 1-10.data analysis
DYANA1.5Guntert et al. J. Mol. Biol. 1997, 273, 283-298.structure solution
CNS1.1Brunger et al. Acta Crystallogr. D, 1998, 54, 905-921.refinement
RefinementMethod: distance geometry torsion angle dynamics simulated annealing
Software ordinal: 1
Details: the structures are based on a total of 3871 constraints. Distance constraints: 694 intraresidue; 843 sequential; 912 short range; 993 long range; 64 hydrogen bonds Dihedral angle constraints: ...Details: the structures are based on a total of 3871 constraints. Distance constraints: 694 intraresidue; 843 sequential; 912 short range; 993 long range; 64 hydrogen bonds Dihedral angle constraints: 136 phi constraints; 101 psi constraints; 34 chi1 constraints; 30 chi2 constraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 256 / Conformers submitted total number: 20

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