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- PDB-3spf: Crystal Structure of Bcl-xL bound to BM501 -

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Basic information

Entry
Database: PDB / ID: 3spf
TitleCrystal Structure of Bcl-xL bound to BM501
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS REGULATOR/INHIBITOR / Bcl-2-like protein / APOPTOSIS-APOPTOSIS INHIBITOR complex / APOPTOSIS REGULATOR-INHIBITOR complex
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / apoptotic mitochondrial changes / germ cell development / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / defense response to virus / nuclear membrane / mitochondrial inner membrane / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / Blc2-like / Apoptosis Regulator Bcl-x ...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 / Blc2-like / Apoptosis Regulator Bcl-x / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B50 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold.
Authors: Zhou, H. / Chen, J. / Meagher, J.L. / Yang, C.Y. / Aguilar, A. / Liu, L. / Bai, L. / Cong, X. / Cai, Q. / Fang, X. / Stuckey, J.A. / Wang, S.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 2.0Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_unobs_or_zero_occ_residues / struct_ref_seq / struct_ref_seq_dif
Item: _entity.formula_weight / _entity_name_com.name ..._entity.formula_weight / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5706
Polymers19,6771
Non-polymers8935
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.748, 103.748, 35.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 19676.582 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pHIS-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q07817
#2: Chemical ChemComp-B50 / 4-(4-chlorophenyl)-1-[(3S)-3,4-dihydroxybutyl]-N-[3-(4-methylpiperazin-1-yl)propyl]-3-phenyl-1H-pyrrole-2-carboxamide


Mass: 525.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H37ClN4O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFRAGMENT COMPRISES UNP Q07817 ISOFORM BCL-X(L) RESIDUES 1-44 AND 85-209 WITH RESIDUES 45-84 DELETED.

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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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 1.2 M sodium citrate, 25 mM CHES, pH 9.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 23, 2008 / Details: mirrors
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 22006 / Num. obs: 21786 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Rmerge(I) obs: 0.052 / Χ2: 1.054 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7314.40.40810570.6681100
1.73-1.7614.50.33710800.6691100
1.76-1.7914.40.30310640.6971100
1.79-1.8314.50.27210550.71100
1.83-1.8714.50.22210710.7291100
1.87-1.9114.60.1910610.741100
1.91-1.9614.50.15210870.7781100
1.96-2.0214.60.11810480.7761100
2.02-2.0714.50.10211050.8431100
2.07-2.1414.60.08410540.8481100
2.14-2.2214.50.07110950.8611100
2.22-2.3114.60.06410680.9251100
2.31-2.4114.50.05810871.0311100
2.41-2.5414.40.05510911.1441100
2.54-2.714.40.05210961.2731100
2.7-2.9114.30.05610981.6731100
2.91-3.214.10.05311042.0251100
3.2-3.6613.90.04511112.0821100
3.66-4.6113.80.03311411.427199.9
4.61-5012.60.02912131.186198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.1data extraction
MD2data collection
HKL-2000data reduction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.9531 / Cor.coef. Fo:Fc free: 0.9378 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.096 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 1116 5.12 %RANDOM
Rwork0.1844 ---
obs0.1854 21781 99.91 %-
all-21800 --
Displacement parametersBiso max: 121.31 Å2 / Biso mean: 31.2307 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1--1.5444 Å20 Å20 Å2
2---1.5444 Å20 Å2
3---3.0888 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1143 0 61 110 1314
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d563SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes33HARMONIC2
X-RAY DIFFRACTIONt_gen_planes190HARMONIC5
X-RAY DIFFRACTIONt_it1303HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion146SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1609SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1303HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg1764HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion2.72
LS refinement shellResolution: 1.7→1.78 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2056 136 4.8 %
Rwork0.1884 2698 -
all0.1892 2834 -
obs--99.91 %
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)
13.1924-0.34330.74020.86240.08510.7904-0.0747-0.3075-0.08330.21970.1735-0.288-0.1288-0.0341-0.0988-0.00330.0477-0.03470.0112-0.0125-0.029636.54919.0955-5.2778
25.56860.32922.01653.4891.26883.72030.1417-0.3162-0.1137-0.1261-0.0006-0.2181-0.0937-0.0993-0.1411-0.01420.0350.0161-0.0291-0.0018-0.06431.920421.86-17.1633
33.771.4258-1.11673.5719-1.95093.7333-0.0901-0.0467-0.4137-0.22050.32950.25770.3828-0.1841-0.2395-0.0197-0.0098-0.0113-0.0390.02650.063129.91153.8382-14.9412
43.4519-0.9194-0.94662.2544-0.03341.5861-0.1738-0.1154-0.27960.150.1590.00130.0918-0.06910.0148-0.04870.0268-0.0032-0.06860.0067-0.04435.07511.3897-11.5421
52.31942.3207-0.33062.4791-0.82841.72360.0592-0.04390.33730.01150.06420.182-0.27370.031-0.1234-0.0331-0.00280.0997-0.0191-0.04180.07247.088821.174-20.6902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 25}A0 - 25
2X-RAY DIFFRACTION2{A|82 - 110}A82 - 110
3X-RAY DIFFRACTION3{A|111 - 133}A111 - 133
4X-RAY DIFFRACTION4{A|134 - 181}A134 - 181
5X-RAY DIFFRACTION5{A|182 - 197}A182 - 197

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