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- PDB-9o14: Crystal Structure of BCL-2 in complex with a stapled BAD BH3 pept... -

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Basic information

Entry
Database: PDB / ID: 9o14
TitleCrystal Structure of BCL-2 in complex with a stapled BAD BH3 peptide BAD SAHB 4.2
Components
  • Apoptosis regulator Bcl-2,Bcl-2-like protein 1
  • stapled BAD BH3 peptide BAD SAHB 4.2
KeywordsAPOPTOSIS / Apoptosis regulator / stapled peptide
Function / homology
Function and homology information


BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / hair follicle morphogenesis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / hair follicle morphogenesis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / pigmentation / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of mitochondrial membrane permeability / B cell proliferation / apoptotic mitochondrial changes / response to iron ion / Bcl-2 family protein complex / negative regulation of mitochondrial depolarization / pore complex / NFE2L2 regulating tumorigenic genes / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / humoral immune response / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of B cell proliferation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuron apoptotic process / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / response to cytokine / B cell receptor signaling pathway / regulation of mitochondrial membrane potential / negative regulation of autophagy / protein phosphatase 2A binding / regulation of cytokinesis / response to nicotine / intrinsic apoptotic signaling pathway in response to DNA damage / female pregnancy / response to radiation / response to toxic substance / protein polyubiquitination / RAS processing / synaptic vesicle membrane / myelin sheath / positive regulation of cell growth / negative regulation of neuron apoptotic process / defense response to virus / nuclear membrane / channel activity / protease binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / sequence-specific DNA binding / Estrogen-dependent gene expression / molecular adaptor activity / apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / ubiquitin protein ligase binding / centrosome / positive regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / 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
NICKEL (II) ION / NITRILOTRIACETIC ACID / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSeo, H.-S. / DeAngelo, T.M. / Bird, G.H. / Walensky, L.D. / Dhe-Paganon, S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into chemoresistance mutants of BCL-2 and their targeting by stapled BAD BH3 helices.
Authors: DeAngelo, T.M. / Adhikary, U. / Korshavn, K.J. / Seo, H.S. / Brotzen-Smith, C.R. / Camara, C.M. / Dhe-Paganon, S. / Bird, G.H. / Wales, T.E. / Walensky, L.D.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
B: stapled BAD BH3 peptide BAD SAHB 4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4475
Polymers22,1392
Non-polymers3093
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-28 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 58.530, 61.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19357.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10415, UniProt: Q07817
#2: Protein/peptide stapled BAD BH3 peptide BAD SAHB 4.2


Mass: 2781.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 15.0% PEG-3350 and 150 mM CsCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.73→38.84 Å / Num. obs: 20222 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.049 / Rrim(I) all: 0.133 / Net I/σ(I): 9 / Num. measured all: 146346
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 2.053 / Num. measured all: 6910 / Num. unique obs: 976 / CC1/2: 0.3 / Rpim(I) all: 1.01 / Rrim(I) all: 2.699 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→32.85 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1017 5.04 %
Rwork0.1948 --
obs0.1962 20172 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 15 104 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031410
X-RAY DIFFRACTIONf_angle_d0.6411900
X-RAY DIFFRACTIONf_dihedral_angle_d14.44510
X-RAY DIFFRACTIONf_chiral_restr0.038187
X-RAY DIFFRACTIONf_plane_restr0.005246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.820.33291170.29792706X-RAY DIFFRACTION100
1.82-1.940.27861640.25242665X-RAY DIFFRACTION100
1.94-2.080.28251410.21132709X-RAY DIFFRACTION100
2.08-2.290.22341390.1872716X-RAY DIFFRACTION100
2.29-2.630.19281480.18282721X-RAY DIFFRACTION100
2.63-3.310.2571400.19622770X-RAY DIFFRACTION100
3.31-32.850.19441680.1822868X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1863-0.4481-0.9532.1791-1.1061.83650.0245-0.0253-0.3801-0.1575-0.05810.13230.7404-0.2860.00070.2662-0.0258-0.00640.25940.02740.2915-2.235-3.2025.67
20.988-0.35210.10370.81480.16641.73880.3686-0.3841-0.39070.3396-0.3201-0.30760.6792-0.11970.00630.29640.02610.00980.29920.04970.32239.694-4.1254.363
30.3588-0.3576-0.00990.361-0.04090.51750.52870.0901-0.3080.1631-0.6802-0.2228-0.75240.21330.00270.4108-0.0009-0.03330.3690.04090.322611.9319.515.028
40.67150.14910.55920.4477-0.20870.960.11980.10470.50490.1418-0.06630.1808-0.4409-0.38660.00630.24970.00380.02540.2819-0.02990.279-0.08116.5758.808
51.6459-0.39340.20590.93130.07731.07130.0209-0.0108-0.0090.0950.0593-0.0569-0.0249-0.0722-0.00030.22890.01280.00960.1964-0.00520.23365.7887.9594.474
63.0051-0.4003-1.86542.7210.67193.23390.01160.002-0.0664-0.08780.0452-0.10930.08760.1489-0.00030.1835-0.0051-0.01360.2073-0.0080.18382.2964.079-1.562
71.34030.8586-0.37740.9325-0.95991.45520.0011-0.05720.0793-0.0339-0.0681-0.4056-0.0830.23530.00010.2457-0.0153-0.01870.30560.01320.260714.29812.8685.309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:32 )A9 - 32
2X-RAY DIFFRACTION2( CHAIN A AND RESID 92:107 )A92 - 107
3X-RAY DIFFRACTION3( CHAIN A AND RESID 108:117 )A108 - 117
4X-RAY DIFFRACTION4( CHAIN A AND RESID 118:137 )A118 - 137
5X-RAY DIFFRACTION5( CHAIN A AND RESID 138:163 )A138 - 163
6X-RAY DIFFRACTION6( CHAIN A AND RESID 164:206 )A164 - 206
7X-RAY DIFFRACTION7( CHAIN B AND RESID 303:323 )B303 - 323

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