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- PDB-4hnj: Crystallographic structure of BCL-xL domain-swapped dimer in comp... -

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Basic information

Entry
Database: PDB / ID: 4hnj
TitleCrystallographic structure of BCL-xL domain-swapped dimer in complex with PUMA BH3 peptide at 2.9A resolution
Components
  • Bcl-2-binding component 3
  • Bcl-2-like protein 1
KeywordsApoptosis/PROTEIN BINDING / BCL2-family / domain-swapped dimer / apoptosis regulation / BCL-xL / PUMA / Apoptosis-PROTEIN BINDING complex
Function / homology
Function and homology information


positive regulation of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / T cell apoptotic process ...positive regulation of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitochondrial membrane permeability / negative regulation of execution phase of apoptosis / fertilization / positive regulation of thymocyte apoptotic process / regulation of growth / fibroblast apoptotic process / Activation of PUMA and translocation to mitochondria / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / execution phase of apoptosis / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of release of cytochrome c from mitochondria / germ cell development / apoptotic mitochondrial changes / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of anoikis / BH3 domain binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / ectopic germ cell programmed cell death / 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 / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / negative regulation of autophagy / release of cytochrome c from mitochondria / response to endoplasmic reticulum stress / epithelial cell proliferation / cellular response to ionizing radiation / regulation of cytokinesis / determination of adult lifespan / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / synaptic vesicle membrane / positive regulation of neuron apoptotic process / channel activity / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / spermatogenesis / cellular response to hypoxia / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / DNA damage response / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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 ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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
Similarity search - Domain/homology
Bcl-2-like protein 1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFisher, J.C. / Yun, M.K. / White, S.W.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: PUMA binding induces partial unfolding within BCL-xL to disrupt p53 binding and promote apoptosis.
Authors: Follis, A.V. / Chipuk, J.E. / Fisher, J.C. / Yun, M.K. / Grace, C.R. / Nourse, A. / Baran, K. / Ou, L. / Min, L. / White, S.W. / Green, D.R. / Kriwacki, R.W.
History
DepositionOct 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Nov 15, 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 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: Bcl-2-like protein 1
C: Bcl-2-binding component 3


Theoretical massNumber of molelcules
Total (without water)50,3933
Polymers50,3933
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.829, 94.829, 111.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

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


Mass: 23669.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide Bcl-2-binding component 3 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 3053.326 Da / Num. of mol.: 1 / Fragment: BH3 domain peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M CaCl2, 0.1 M NaOAc, 20% V/V isopropanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 21, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 11798 / Num. obs: 11326 / % possible obs: 96 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34 / Redundancy: 21.7 % / Rsym value: 0.094 / Net I/σ(I): 38.5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allDiffraction-ID% possible all
2.9-38.8788168.9
3-3.129.81039190.4
3.12-3.2712.71150199.4
3.27-3.6520.423171100
3.65-4.9628.335171100
4.96-5026.72515199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R2D

1r2d


Resolution: 2.9→42.878 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7923 / SU ML: 0.42 / σ(F): 1.34 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 542 4.82 %RANDOM
Rwork0.2057 ---
obs0.2079 11256 95.49 %-
all-11788 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.845 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 197.81 Å2 / Biso mean: 93.8646 Å2 / Biso min: 34.81 Å2
Baniso -1Baniso -2Baniso -3
1-9.0736 Å20 Å2-0 Å2
2--9.0736 Å2-0 Å2
3----18.1471 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 0 4 2334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042381
X-RAY DIFFRACTIONf_angle_d0.7753221
X-RAY DIFFRACTIONf_chiral_restr0.05341
X-RAY DIFFRACTIONf_plane_restr0.002416
X-RAY DIFFRACTIONf_dihedral_angle_d15.017824
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.19560.36171370.27632253239083
3.1956-3.65770.21791290.192745287499
3.6577-4.60750.21881390.153827722911100
4.6075-42.88290.26431370.23182944308199
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)
12.7994-0.89120.57711.5291-0.14843.15770.30420.21920.1363-0.211-0.08430.1449-0.3285-0.3133-0.20680.47580.10670.02880.4124-0.00520.408142.17974.0749-13.7386
23.0632-0.53030.16573.27140.12872.5659-0.3395-0.40890.2832-0.4812-0.2171-0.1514-0.520.60890.08890.55940.3216-0.06330.66740.02390.425732.050926.2863-28.7465
34.5473.53644.51063.43713.42584.4945-0.1767-0.52111.01730.1637-0.12610.5425-0.4536-0.69680.74990.6390.38810.0480.99740.00730.749224.896616.6157-12.3952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA-1 - 196
2X-RAY DIFFRACTION2CHAIN BB-1 - 195
3X-RAY DIFFRACTION3CHAIN CC302 - 323

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