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- PDB-6ckv: Solution NMR structure of human BOK -

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Basic information

Entry
Database: PDB / ID: 6ckv
TitleSolution NMR structure of human BOK
ComponentsBcl-2-related ovarian killer protein
KeywordsAPOPTOSIS
Function / homology
Function and homology information


cellular component disassembly involved in execution phase of apoptosis / regulation of granulosa cell apoptotic process / regulation of chorionic trophoblast cell proliferation / positive regulation of PERK-mediated unfolded protein response / cis-Golgi network membrane / BH domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...cellular component disassembly involved in execution phase of apoptosis / regulation of granulosa cell apoptotic process / regulation of chorionic trophoblast cell proliferation / positive regulation of PERK-mediated unfolded protein response / cis-Golgi network membrane / BH domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of necroptotic process / nuclear outer membrane / negative regulation of mitochondrial depolarization / oligodendrocyte differentiation / positive regulation of execution phase of apoptosis / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / regulation of cytosolic calcium ion concentration / release of cytochrome c from mitochondria / trans-Golgi network membrane / regulation of autophagy / mitochondrial membrane / brain development / recycling endosome membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / protein complex oligomerization / early endosome membrane / neuron apoptotic process / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / membrane => GO:0016020 / positive regulation of apoptotic process / protein heterodimerization activity / signaling receptor binding / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / mitochondrion / membrane / nucleus / cytoplasm
Similarity search - Function
Bcl-2-related ovarian killer protein / 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
Similarity search - Domain/homology
Bcl-2-related ovarian killer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGrace, C.R. / Zheng, J. / Moldoveanu, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA021765-36 United States
CitationJournal: Cell Rep / Year: 2018
Title: Intrinsic Instability of BOK Enables Membrane Permeabilization in Apoptosis.
Authors: Zheng, J.H. / Grace, C.R. / Guibao, C.D. / McNamara, D.E. / Llambi, F. / Wang, Y.M. / Chen, T. / Moldoveanu, T.
History
DepositionMar 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization ..._pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-related ovarian killer protein


Theoretical massNumber of molelcules
Total (without water)17,1861
Polymers17,1861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9180 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Bcl-2-related ovarian killer protein / hBOK / Bcl-2-like protein 9 / Bcl2-L-9


Mass: 17186.006 Da / Num. of mol.: 1 / Fragment: residues 21-177 / Mutation: C67A, P100R, C137A, C152A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BOK, BCL2L9 / Production host: Escherichia coli 536 (bacteria) / References: UniProt: Q9UMX3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D-15N-NOESY
121isotropic13D-13C-NOESY
131isotropic13D-NOESY-aro
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-99% 13C; U-99% 15N] hBOK, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: hBOK / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.8 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CARA1.9Keller and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9Keller and Wuthrichpeak picking
TopSpin3.5Bruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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