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- PDB-4qve: Crystal structure of Bcl-xL in complex with BID BH3 domain -

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Basic information

Entry
Database: PDB / ID: 4qve
TitleCrystal structure of Bcl-xL in complex with BID BH3 domain
Components
  • Bcl-2-like protein 1
  • Peptide from BH3-interacting domain death agonist
KeywordsAPOPTOSIS / Protein-peptide complex / Bcl-2 like / Heterodimer / Anti-apoptotic / BH3 binding / BID BH3
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / 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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / protein targeting to mitochondrion / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of epithelial cell proliferation / establishment of protein localization to membrane / death receptor binding / fertilization / positive regulation of extrinsic apoptotic signaling pathway / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / positive regulation of mitochondrial membrane potential / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / regulation of T cell proliferation / 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 / regulation of G1/S transition of mitotic cell cycle / germ cell development / apoptotic mitochondrial changes / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / mitochondrial ATP synthesis coupled electron transport / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Activation of BAD and translocation to mitochondria / ectopic germ cell programmed cell death / signal transduction in response to DNA damage / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / supramolecular fiber organization / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of 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 / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / protein-containing complex assembly / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / protein heterodimerization activity / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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 ...BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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 (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
Similarity search - Domain/homology
IMIDAZOLE / BH3-interacting domain death agonist / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSreekanth, R. / Yoon, H.S.
CitationJournal: Proteins / Year: 2015
Title: Bh3 induced conformational changes in Bcl-Xl revealed by crystal structure and comparative analysis.
Authors: Rajan, S. / Choi, M. / Baek, K. / Yoon, H.S.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bcl-2-like protein 1
B: Peptide from BH3-interacting domain death agonist
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0753
Polymers23,0062
Non-polymers691
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-16 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.760, 63.760, 187.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-113-

HIS

21A-394-

HOH

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Components

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


Mass: 19313.217 Da / Num. of mol.: 1 / Fragment: UNP residues 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pETSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide Peptide from BH3-interacting domain death agonist / p22 BID / BID / BH3-interacting domain death agonist p15 / p15 BID / BH3-interacting domain death ...p22 BID / BID / BH3-interacting domain death agonist p15 / p15 BID / BH3-interacting domain death agonist p13 / p13 BID / BH3-interacting domain death agonist p11 / p11 BID


Mass: 3693.111 Da / Num. of mol.: 1 / Fragment: BID BH3, UNP RESIDUES 76-109 / Source method: obtained synthetically / Details: This BID BH3 sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 2.0M Ammonium Sulphate, 0.2M Lithium Sulphate, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→37.86 Å / Num. obs: 16313 / % possible obs: 99.9 % / Biso Wilson estimate: 22.82 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 9
Reflection shellResolution: 2.05→2.11 Å / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2299 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EHR

4ehr


Resolution: 2.05→26.486 Å / SU ML: 0.22 / σ(F): 1.67 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 750 5.07 %
Rwork0.179 --
obs0.1813 14799 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→26.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 5 136 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081368
X-RAY DIFFRACTIONf_angle_d0.951850
X-RAY DIFFRACTIONf_dihedral_angle_d13.139488
X-RAY DIFFRACTIONf_chiral_restr0.042193
X-RAY DIFFRACTIONf_plane_restr0.004243

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