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- PDB-8vwx: Human Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to Maltose-Bindin... -

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Basic information

Entry
Database: PDB / ID: 8vwx
TitleHuman Bcl-2 (G101V Mutant)/Bcl-xL Chimera Fused to Maltose-Binding Protein
ComponentsMaltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera
KeywordsAPOPTOSIS / Bcl-2 / G101V Mutant / MBP Fusion / Bcl-xL Chimera
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 / NFE2L2 regulating tumorigenic genes / pore complex / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / detection of maltose stimulus / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / carbohydrate transport / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / 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 / carbohydrate transmembrane transporter activity / maltose binding / neuron apoptotic process / negative regulation of protein localization to plasma membrane / maltose transport / maltodextrin transmembrane transport / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / B cell receptor signaling pathway / regulation of mitochondrial membrane potential / negative regulation of autophagy / ATP-binding cassette (ABC) transporter complex / protein phosphatase 2A binding / regulation of cytokinesis / response to nicotine / intrinsic apoptotic signaling pathway in response to DNA damage / cell chemotaxis / female pregnancy / myelin sheath / endocytosis / response to radiation / response to toxic substance / protein polyubiquitination / RAS processing / synaptic vesicle membrane / positive regulation of cell growth / negative regulation of neuron apoptotic process / outer membrane-bounded periplasmic space / nuclear membrane / defense response to virus / channel activity / protease binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / molecular adaptor activity / mitochondrial outer membrane / periplasmic space / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / 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
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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBaird, J. / Holliday, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Anal.Chem. / Year: 2025
Title: Hydrogen/Deuterium Exchange and Protein Oxidative Footprinting with Mass Spectrometry Collectively Discriminate the Binding of Small-Molecule Therapeutics to Bcl-2.
Authors: Sun, Y. / Houde, D. / Iacob, R.E. / Baird, J. / Swift, R.V. / Holliday, M. / Shi, X. / Sidoli, S. / Brenowitz, M.
History
DepositionFeb 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera


Theoretical massNumber of molelcules
Total (without water)61,3031
Polymers61,3031
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.343, 89.031, 142.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 61302.895 Da / Num. of mol.: 1 / Mutation: G101V
Source method: isolated from a genetically manipulated source
Details: For the alignment, MBP (UNP P0AEX9, 27-392) spans residues 19-384 (w/ surface entropy reduction mutations at 100, 101, 190, 191, and 257) and is fused to a Bcl-2/Bcl-xL chimera via a linker ...Details: For the alignment, MBP (UNP P0AEX9, 27-392) spans residues 19-384 (w/ surface entropy reduction mutations at 100, 101, 190, 191, and 257) and is fused to a Bcl-2/Bcl-xL chimera via a linker sequence (AARAAA) spanning 385-390. Bcl-2 (UNP P10415, 10-207, G101V mutation) has the unstructured loop spanning 35-91 deleted and replaced with Bcl-xL (UNP Q07817, 29-44) for residues 35-50 of the Bcl-2/Bcl-xL chimera, so Bcl-2 spans 391-415 and 432-547, while Bcl-xL spans 416-431. For the 3D model, MBP (-362-3), linker (4-9), Bcl-2 (10-34 and 92-207), and Bcl-xL (35-50). GLU91 of the final model corresponds to residue 50 (Bcl-xL) of the loop replacement (35-50).
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, BCL2, BCL2L1, BCL2L, BCLX / Plasmid: pET-24b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: P10415, UniProt: Q07817
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris (pH 8.5), 25% PEG 3350, and 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.77→42.48 Å / Num. obs: 47261 / % possible obs: 99.96 % / Redundancy: 7.2 % / Biso Wilson estimate: 25.79 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1294 / Rpim(I) all: 0.05167 / Rrim(I) all: 0.1395 / Net I/σ(I): 10.26
Reflection shellResolution: 1.77→1.833 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 4625 / CC1/2: 0.352 / CC star: 0.721 / Rpim(I) all: 0.86 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→42.48 Å / SU ML: 0.2317 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.0706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2246 2414 5.11 %
Rwork0.1912 44837 -
obs0.1929 47251 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.4 Å2
Refinement stepCycle: LAST / Resolution: 1.77→42.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 0 413 4363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324087
X-RAY DIFFRACTIONf_angle_d0.56225555
X-RAY DIFFRACTIONf_chiral_restr0.0412594
X-RAY DIFFRACTIONf_plane_restr0.0044722
X-RAY DIFFRACTIONf_dihedral_angle_d21.05761475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.36871530.33332562X-RAY DIFFRACTION100
1.81-1.850.33971240.32342613X-RAY DIFFRACTION99.89
1.85-1.890.30771300.30762623X-RAY DIFFRACTION99.96
1.89-1.940.27681350.25542600X-RAY DIFFRACTION99.93
1.94-1.990.29581360.23942593X-RAY DIFFRACTION99.93
1.99-2.050.28031500.22952589X-RAY DIFFRACTION99.93
2.05-2.110.25611340.23092609X-RAY DIFFRACTION99.96
2.11-2.190.24391330.21432630X-RAY DIFFRACTION99.96
2.19-2.280.22821560.19612577X-RAY DIFFRACTION99.96
2.28-2.380.23141720.19052610X-RAY DIFFRACTION100
2.38-2.50.23081530.18132622X-RAY DIFFRACTION100
2.5-2.660.18931170.1832660X-RAY DIFFRACTION99.96
2.66-2.870.24651380.18822655X-RAY DIFFRACTION100
2.87-3.160.22851420.18762644X-RAY DIFFRACTION99.96
3.16-3.610.2131620.17772647X-RAY DIFFRACTION99.86
3.61-4.550.18981380.15652728X-RAY DIFFRACTION100
4.55-42.480.1861410.16732875X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 7.01881203175 Å / Origin y: 8.12743904445 Å / Origin z: 19.4730354864 Å
111213212223313233
T0.153506039595 Å2-0.00121008079376 Å20.00438685872081 Å2-0.185219244553 Å20.00217757310376 Å2--0.225592861037 Å2
L0.291498135674 °20.00318523440275 °2-0.216728421337 °2-0.883212768884 °2-0.0118353103471 °2--0.784614698501 °2
S-0.00218077143645 Å °0.0414569971687 Å °-0.00533225564718 Å °-0.0336066474371 Å °-0.00646805056878 Å °0.0395098586685 Å °0.107548484633 Å °0.0135297754512 Å °0.00904724640206 Å °
Refinement TLS groupSelection details: all

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