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- PDB-8vxn: Human Bcl-2/Bcl-xL Chimera Fused to Maltose-Binding Protein -

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Basic information

Entry
Database: PDB / ID: 8vxn
TitleHuman Bcl-2/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 / MBP Fusion / Bcl-xL Chimera
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 / channel inhibitor activity / melanin metabolic process ...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 / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / gland morphogenesis / apoptotic process in bone marrow cell / renal system process / regulation of cell-matrix adhesion / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / negative regulation of calcium ion transport into cytosol / SARS-CoV-1-mediated effects on programmed cell death / lymphoid progenitor cell differentiation / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 / negative regulation of dendritic cell apoptotic process / regulation of nitrogen utilization / glomerulus development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / focal adhesion assembly / negative regulation of T cell apoptotic process / regulation of transmembrane transporter activity / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / response to UV-B / calcium ion transport into cytosol / negative regulation of ossification / response to iron ion / axon regeneration / epithelial cell apoptotic process / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / 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 / organ growth / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / cellular response to alkaloid / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / hepatocyte apoptotic process / B cell lineage commitment / pore complex / detection of maltose stimulus / negative regulation of release of cytochrome c from mitochondria / maltose transport complex / negative regulation of reproductive process / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of developmental process / apoptotic mitochondrial changes / germ cell development / carbohydrate transport / T cell homeostasis / BH3 domain binding / regulation of calcium ion transport / B cell homeostasis / B cell proliferation / humoral immune response / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors
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: 2.09 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 5, 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)61,2611
Polymers61,2611
Non-polymers00
Water2,414134
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)37.070, 88.950, 140.940
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: 61260.816 Da / Num. of mol.: 1
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) 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.: 134 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 29% PEG 3350, 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.005→75.222 Å / Num. obs: 29956 / % possible obs: 93 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 2.005→2.04 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1591 / CC1/2: 0.852 / Rpim(I) all: 0.338 / Rrim(I) all: 0.89 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.1.7data reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→55.24 Å / SU ML: 0.263 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 1366 4.94 %
Rwork0.2036 26294 -
obs0.2064 27660 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.65 Å2
Refinement stepCycle: LAST / Resolution: 2.09→55.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 0 134 4096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344063
X-RAY DIFFRACTIONf_angle_d0.55285515
X-RAY DIFFRACTIONf_chiral_restr0.0422588
X-RAY DIFFRACTIONf_plane_restr0.0042715
X-RAY DIFFRACTIONf_dihedral_angle_d18.38711463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.160.31611410.2532662X-RAY DIFFRACTION99.89
2.16-2.250.31461390.23832439X-RAY DIFFRACTION99.5
2.25-2.350.26821320.23842560X-RAY DIFFRACTION99.52
2.35-2.480.3111430.2332682X-RAY DIFFRACTION99.93
2.48-2.630.31281360.2312678X-RAY DIFFRACTION99.68
2.63-2.840.32561370.23082349X-RAY DIFFRACTION87.81
2.84-3.120.26071290.2272697X-RAY DIFFRACTION99.96
3.12-3.570.27881480.21542705X-RAY DIFFRACTION99.72
3.57-4.50.23771300.17712603X-RAY DIFFRACTION94.37
4.5-55.240.21741310.17542919X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 7.22774740958 Å / Origin y: 7.93514182339 Å / Origin z: 18.8073890097 Å
111213212223313233
T0.228353617105 Å20.0035323713978 Å2-0.00268828251064 Å2-0.231020692311 Å20.00139084662161 Å2--0.343904067555 Å2
L0.401909917451 °2-0.0196645391381 °2-0.134219251289 °2-1.66888136407 °20.208048341306 °2--0.871473788956 °2
S0.00311026977735 Å °0.0795049574767 Å °0.00504390472296 Å °-0.11872531933 Å °0.00382850063159 Å °0.0287908235961 Å °0.126035477624 Å °-0.010106503496 Å °-0.00614320680228 Å °
Refinement TLS groupSelection details: all

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