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- PDB-5jsn: Bcl2-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5jsn
TitleBcl2-inhibitor complex
Components
  • Apoptosis regulator Bcl-2
  • Bcl2 inhibitor
KeywordsViral Protein/Inhibitor / Bcl-2 / antiBcl2 / complex / Viral Protein-Inhibitor complex
Function / homology
Function and homology information


: / negative regulation of retinal cell programmed cell death / pigment granule organization / BCL-2 complex / 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 ...: / negative regulation of retinal cell programmed cell death / pigment granule organization / BCL-2 complex / 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 / myeloid cell apoptotic process / positive regulation of neuron maturation / channel inhibitor activity / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / renal system process / gland morphogenesis / dendritic cell apoptotic process / regulation of cell-matrix adhesion / negative regulation of T cell apoptotic process / The NLRP1 inflammasome / ear development / negative regulation of calcium ion transport into cytosol / T cell apoptotic process / negative regulation of epithelial cell apoptotic process / negative regulation of myeloid cell apoptotic process / lymphoid progenitor cell differentiation / melanocyte differentiation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / organ growth / negative regulation of dendritic cell apoptotic process / oocyte development / regulation of nitrogen utilization / neuron maturation / focal adhesion assembly / negative regulation of motor neuron apoptotic process / glomerulus development / metanephros development / positive regulation of multicellular organism growth / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / epithelial cell apoptotic process / motor neuron apoptotic process / calcium ion transport into cytosol / hair follicle morphogenesis / regulation of mitochondrial membrane permeability / negative regulation of ossification / response to iron ion / response to UV-B / axon regeneration / negative regulation of mitochondrial depolarization / intrinsic apoptotic signaling pathway in response to oxidative stress / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / negative regulation of B cell apoptotic process / branching involved in ureteric bud morphogenesis / positive regulation of smooth muscle cell migration / digestive tract morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of G1/S transition of mitotic cell cycle / B cell lineage commitment / B cell homeostasis / negative regulation of intrinsic apoptotic signaling pathway / pore complex / T cell homeostasis / humoral immune response / extrinsic apoptotic signaling pathway via death domain receptors / regulation of calcium ion transport / B cell proliferation / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / hematopoietic stem cell differentiation / BH3 domain binding / negative regulation of apoptotic signaling pathway / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / spleen development / behavioral fear response / ovarian follicle development / cellular response to glucose starvation / homeostasis of number of cells within a tissue / skeletal muscle fiber development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of B cell proliferation / axonogenesis / response to cytokine / reactive oxygen species metabolic process / thymus development / release of cytochrome c from mitochondria / post-embryonic development / response to ischemia / protein phosphatase 2A binding / ossification
Similarity search - Function
Ribosome-recycling factor / Apoptosis regulator, Bcl-2 / 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 ...Ribosome-recycling factor / Apoptosis regulator, Bcl-2 / 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 / Topoisomerase I; Chain A, domain 4 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShen, B.W. / Stoddard, B.L.
CitationJournal: Elife / Year: 2016
Title: Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer.
Authors: Berger, S. / Procko, E. / Margineantu, D. / Lee, E.F. / Shen, B.W. / Zelter, A. / Silva, D.A. / Chawla, K. / Herold, M.J. / Garnier, J.M. / Johnson, R. / MacCoss, M.J. / Lessene, G. / Davis, ...Authors: Berger, S. / Procko, E. / Margineantu, D. / Lee, E.F. / Shen, B.W. / Zelter, A. / Silva, D.A. / Chawla, K. / Herold, M.J. / Garnier, J.M. / Johnson, R. / MacCoss, M.J. / Lessene, G. / Davis, T.N. / Stayton, P.S. / Stoddard, B.L. / Fairlie, W.D. / Hockenbery, D.M. / Baker, D.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2
B: Bcl2 inhibitor
C: Apoptosis regulator Bcl-2
D: Bcl2 inhibitor


Theoretical massNumber of molelcules
Total (without water)75,5764
Polymers75,5764
Non-polymers00
Water2,738152
1
A: Apoptosis regulator Bcl-2
B: Bcl2 inhibitor


Theoretical massNumber of molelcules
Total (without water)37,7882
Polymers37,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-10 kcal/mol
Surface area13410 Å2
MethodPISA
2
C: Apoptosis regulator Bcl-2
D: Bcl2 inhibitor


Theoretical massNumber of molelcules
Total (without water)37,7882
Polymers37,7882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-12 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.005, 65.005, 134.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLUGLUAA7 - 2097 - 209
21THRTHRGLUGLUCC7 - 2097 - 209
12ASPASPTYRTYRBB3 - 1173 - 117
22ASPASPTYRTYRDD3 - 1173 - 117

NCS ensembles :
ID
1
2

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 23932.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10415
#2: Protein Bcl2 inhibitor


Mass: 13854.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.06 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Jeffamine ED-2001, pH7.0/100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 20, 2015
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.692
11-H, K, -L20.308
ReflectionResolution: 2.1→32.5 Å / % possible obs: 96.6 % / Redundancy: 6 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.508 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 29.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 1.68 / % possible all: 69.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000708data reduction
HKL-2000708data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.627 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20534 1605 5 %RANDOM
Rwork0.15927 ---
obs0.1617 30512 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.024 Å2
Baniso -1Baniso -2Baniso -3
1-17.56 Å20 Å20 Å2
2--17.56 Å20 Å2
3----35.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 0 152 4526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194470
X-RAY DIFFRACTIONr_bond_other_d0.0080.024316
X-RAY DIFFRACTIONr_angle_refined_deg2.011.966008
X-RAY DIFFRACTIONr_angle_other_deg1.73439880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42923.036247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69515838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5491555
X-RAY DIFFRACTIONr_chiral_restr0.1260.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025034
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021097
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4523.2982113
X-RAY DIFFRACTIONr_mcbond_other2.4523.2982112
X-RAY DIFFRACTIONr_mcangle_it3.524.9232633
X-RAY DIFFRACTIONr_mcangle_other3.5194.9232634
X-RAY DIFFRACTIONr_scbond_it2.7443.6862357
X-RAY DIFFRACTIONr_scbond_other2.7433.6862358
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1795.4013375
X-RAY DIFFRACTIONr_long_range_B_refined6.60226.5145319
X-RAY DIFFRACTIONr_long_range_B_other6.57726.3935292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A157440.14
12C157440.14
21B131060.16
22D131060.16
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 123 -
Rwork0.254 2108 -
obs--94.41 %
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)
11.69930.34650.16162.9680.71573.85070.0310.2036-0.0792-0.1102-0.01590.15230.1937-0.2935-0.01510.019-0.0117-0.02350.0499-0.00950.2169-3.5849-5.648258.2767
24.8921-1.2923-1.61372.26640.86143.65270.22510.12550.3492-0.1739-0.0076-0.2213-0.28280.0827-0.21750.0768-0.03580.00580.03090.01080.25087.331510.523258.8693
32.20280.60880.97041.97960.19844.33070.0922-0.17620.1390.1243-0.0236-0.0347-0.11870.329-0.06860.0361-0.01340.04290.0655-0.03160.1736.225437.244972.6643
42.9751-0.95771.33943.2358-2.01373.88760.0989-0.2512-0.26890.10590.09160.27370.1483-0.018-0.19050.0927-0.03380.03190.0455-0.01590.213822.455523.403870.2064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 209
2X-RAY DIFFRACTION2B3 - 117
3X-RAY DIFFRACTION3C7 - 209
4X-RAY DIFFRACTION4D3 - 117

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