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- PDB-6qg8: Structure of human Bcl-2 in complex with PUMA BH3 peptide -

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Basic information

Entry
Database: PDB / ID: 6qg8
TitleStructure of human Bcl-2 in complex with PUMA BH3 peptide
Components
  • Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Bcl-2-like protein 1
  • Bcl-2-binding component 3
KeywordsAPOPTOSIS / MCL1 / BCL2 / PUMA
Function / homology
Function and homology information


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process / positive regulation of neuron maturation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process / positive regulation of neuron maturation / channel inhibitor activity / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / positive regulation of protein localization to mitochondrion / stem cell development / gland morphogenesis / apoptotic process in bone marrow cell / renal system process / regulation of cell-matrix adhesion / dendritic cell apoptotic process / The NLRP1 inflammasome / ear development / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / negative regulation of calcium ion transport into cytosol / SARS-CoV-1-mediated effects on programmed cell death / lymphoid progenitor cell differentiation / melanocyte differentiation / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of nitrogen utilization / glomerulus development / regulation of transmembrane transporter activity / negative regulation of dendritic cell apoptotic process / focal adhesion assembly / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of T cell apoptotic process / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / positive regulation of multicellular organism growth / regulation of viral genome replication / Regulation of MITF-M-dependent genes involved in apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / negative regulation of execution phase of apoptosis / positive regulation of thymocyte apoptotic process / calcium ion transport into cytosol / fertilization / regulation of growth / fibroblast apoptotic process / negative regulation of ossification / response to iron ion / response to UV-B / epithelial cell apoptotic process / Activation of PUMA and translocation to mitochondria / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / axon regeneration / motor neuron apoptotic process / positive regulation of smooth muscle cell migration / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / execution phase of apoptosis / organ growth / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / response to cycloheximide / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / pore complex / cellular response to alkaloid / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / germ cell development / T cell homeostasis / apoptotic mitochondrial changes / B cell homeostasis / negative regulation of reproductive process
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / 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. ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Apoptosis regulator, Bcl-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / 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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Apoptosis regulator Bcl-2 / Bcl-2-like protein 1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDokurno, P. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Graham, C.J. / Harris, R. / Jordan, A.M. / Matassova, N. / Pedder, C. ...Dokurno, P. / Murray, J. / Davidson, J. / Chen, I. / Davis, B. / Graham, C.J. / Harris, R. / Jordan, A.M. / Matassova, N. / Pedder, C. / Ray, S. / Roughley, S. / Smith, J. / Walmsley, C. / Wang, Y. / Whitehead, N. / Williamson, D.S. / Casara, P. / Le Diguarher, T. / Hickman, J. / Stark, J. / Kotschy, A. / Geneste, O. / Hubbard, R.E.
CitationJournal: Acs Omega / Year: 2019
Title: Establishing Drug Discovery and Identification of Hit Series for the Anti-apoptotic Proteins, Bcl-2 and Mcl-1.
Authors: Murray, J.B. / Davidson, J. / Chen, I. / Davis, B. / Dokurno, P. / Graham, C.J. / Harris, R. / Jordan, A. / Matassova, N. / Pedder, C. / Ray, S. / Roughley, S.D. / Smith, J. / Walmsley, C. / ...Authors: Murray, J.B. / Davidson, J. / Chen, I. / Davis, B. / Dokurno, P. / Graham, C.J. / Harris, R. / Jordan, A. / Matassova, N. / Pedder, C. / Ray, S. / Roughley, S.D. / Smith, J. / Walmsley, C. / Wang, Y. / Whitehead, N. / Williamson, D.S. / Casara, P. / Le Diguarher, T. / Hickman, J. / Stark, J. / Kotschy, A. / Geneste, O. / Hubbard, R.E.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 18, 2019Group: Data collection / Refinement description / Category: software / Item: _software.version
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Bcl-2-like protein 1
B: Bcl-2-binding component 3


Theoretical massNumber of molelcules
Total (without water)23,1902
Polymers23,1902
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-12 kcal/mol
Surface area8200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.135, 54.950, 84.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 20442.461 Da / Num. of mol.: 1
Mutation: H20S, L95Q, R106L, F124G, R127Y, G128A, R129S, P168V, L175A, T178A, E179T, R183D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS / References: UniProt: P10415, UniProt: Q07817
#2: Protein/peptide Bcl-2-binding component 3 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 2747.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 284 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: from 0.2M MgCl2, 25% PegMME 2k, 0.1M Na Acetate buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 13577 / % possible obs: 75 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.111 / Χ2: 1.207 / Net I/σ(I): 7.1 / Num. measured all: 47632
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.8-1.861.90.5342940.906116.7
1.86-1.942.40.4966000.972133.5
1.94-2.032.90.3918971.293150.9
2.03-2.133.20.33713351.332174.1
2.13-2.273.50.32416361.37191.9
2.27-2.443.80.24217331.325197.5
2.44-2.693.90.19517581.207197.3
2.69-3.083.80.13717731.165197
3.08-3.883.70.09117541.104195.6
3.88-503.60.05617971.042191.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yxj

2yxj


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.522 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1597 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 647 5 %RANDOM
Rwork0.169 ---
obs0.1713 12321 84.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96 Å2 / Biso mean: 29.333 Å2 / Biso min: 15.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0 Å2
2---1.77 Å20 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 0 135 1405
Biso mean---38.81 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0141316
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171095
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6411784
X-RAY DIFFRACTIONr_angle_other_deg1.081.642550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2435157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67521.59188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77915208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.041512
X-RAY DIFFRACTIONr_chiral_restr0.0770.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
LS refinement shellResolution: 1.9→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.267 52 -
Rwork0.251 898 -
all-950 -
obs--43.56 %

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