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- PDB-1mk3: SOLUTION STRUCTURE OF HUMAN BCL-W PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1mk3
TitleSOLUTION STRUCTURE OF HUMAN BCL-W PROTEIN
ComponentsApoptosis regulator Bcl-W
KeywordsAPOPTOSIS / Bcl-w protein / apoptotis
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / Sertoli cell proliferation / BH domain binding / Bcl-2 family protein complex / cellular response to glycine / negative regulation of release of cytochrome c from mitochondria / 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 / cellular response to glycine / negative regulation of release of cytochrome c from mitochondria / 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 / simulated annealing
AuthorsDenisov, A.Y. / Madiraju, M.S. / Chen, G. / Khadir, A. / Beauparlant, P. / Attardo, G. / Shore, G.C. / Gehring, K.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: Solution structure of human BCL-w: modulation of ligand binding by the C-terminal helix
Authors: Denisov, A.Y. / Madiraju, M.S. / Chen, G. / Khadir, A. / Beauparlant, P. / Attardo, G. / Shore, G.C. / Gehring, K.
History
DepositionAug 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)19,6601
Polymers19,6601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average,lowest energy

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Components

#1: Protein Apoptosis regulator Bcl-W / Bcl-w


Mass: 19659.885 Da / Num. of mol.: 1 / Mutation: P116V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92843

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CB
121CBCA(CO)HN
13113C,15N-edited NOESY
141HNCO
15215N-edited NOESY
162HNHA
173IPAP-HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM Bcl-w protein U-15N,13C, 20 mM phosphate buffer90% H2O/10% D2O
21.3 mM Bcl-w protein U-15N, 20 mM phosphate buffer90% H2O/10% D2O
30.5 mM Bcl-w protein U-15N, 6 MG/ML PF1-PHAGE90% H2O/10% D2O
Sample conditionsIonic strength: 10 mM NaCl / pH: 7.3 / Pressure: 1 atm / Temperature: 298 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrungercollection
CNSBrungerprocessing
CNSBrungerdata analysis
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure refined by using standard protocol in CNS with restraints from NOE distances, backbone torsion angles, hydrogen bonds and residual dipolar couplings
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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