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- PDB-7wjh: Crystal structure of Bcl-xL bound to the BH3 domain of human Pxt1 -

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Basic information

Entry
Database: PDB / ID: 7wjh
TitleCrystal structure of Bcl-xL bound to the BH3 domain of human Pxt1
Components
  • Bcl-2-like protein 1
  • Peroxisomal testis-specific protein 1
KeywordsAPOPTOSIS / Peroxisomal testis-specific 1 / Pxt1 / Bcl-XL / BH3
Function / homology
Function and homology information


The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of synaptic vesicle endocytosis / positive regulation of mononuclear cell proliferation / 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 / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / regulation of growth / negative regulation of protein localization to plasma membrane / Bcl-2 family protein complex / BH domain binding / response to cycloheximide / clathrin binding / regulation of long-term synaptic depression / positive regulation of ATP biosynthetic process / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / 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 / extrinsic apoptotic signaling pathway in absence of ligand / MDM2/MDM4 family protein binding / release of cytochrome c from mitochondria / regulation of cytokinesis / regulation of mitochondrial membrane potential / mitochondrion organization / epithelial cell proliferation / response to cytokine / response to ischemia / mitochondrial membrane / cellular response to amino acid stimulus / response to virus / response to radiation / cellular response to gamma radiation / synaptic vesicle membrane / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / GTPase binding / peroxisome / presynapse / spermatogenesis / nuclear membrane / neuron apoptotic process / regulation of apoptotic process / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / centrosome / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
Peroxisomal testis-specific protein 1 / Peroxisomal testis-specific protein 1 / 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 ...Peroxisomal testis-specific protein 1 / Peroxisomal testis-specific protein 1 / 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
Bcl-2-like protein 1 / Peroxisomal testis-specific protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsLim, D. / Ku, B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019M3E5D6063955 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Structural and biochemical analyses of Bcl-xL in complex with the BH3 domain of peroxisomal testis-specific 1.
Authors: Lim, D. / Jin, S. / Shin, H.C. / Kim, W. / Choi, J.S. / Oh, D.B. / Kim, S.J. / Seo, J. / Ku, B.
History
DepositionJan 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1
B: Peroxisomal testis-specific protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4224
Polymers21,3022
Non-polymers1202
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-37 kcal/mol
Surface area9290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.658, 60.675, 97.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

21A-422-

HOH

31A-471-

HOH

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Components

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


Mass: 18124.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl2l1, Bcl2l, Bclx / Production host: Escherichia coli (E. coli) / References: UniProt: Q64373
#2: Protein/peptide Peroxisomal testis-specific protein 1 / Small testis-specific peroxisomal protein


Mass: 3176.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NFP0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate and 30% (w/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.698→50 Å / Num. obs: 18530 / % possible obs: 97.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 33.7
Reflection shellResolution: 1.698→1.73 Å / Num. unique obs: 948 / CC1/2: 0.371

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BZW

2bzw


Resolution: 1.698→25.6119 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1869 10.09 %
Rwork0.1716 --
obs0.1751 18528 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→25.6119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1425 0 6 185 1616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061460
X-RAY DIFFRACTIONf_angle_d0.751973
X-RAY DIFFRACTIONf_dihedral_angle_d16.481853
X-RAY DIFFRACTIONf_chiral_restr0.047205
X-RAY DIFFRACTIONf_plane_restr0.005259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6982-1.74410.2461590.20691261X-RAY DIFFRACTION98
1.7441-1.79540.2351410.18931296X-RAY DIFFRACTION99
1.7954-1.85330.20871370.17781255X-RAY DIFFRACTION99
1.8533-1.91960.23031350.17491293X-RAY DIFFRACTION99
1.9196-1.99640.21121490.17451283X-RAY DIFFRACTION99
1.9964-2.08720.20411430.16911290X-RAY DIFFRACTION99
2.0872-2.19720.19031470.16571281X-RAY DIFFRACTION99
2.1972-2.33480.22181380.16041279X-RAY DIFFRACTION98
2.3348-2.51490.231420.17591278X-RAY DIFFRACTION98
2.5149-2.76770.19411510.16991289X-RAY DIFFRACTION98
2.7677-3.16760.22291450.17691280X-RAY DIFFRACTION97
3.1676-3.98840.18131370.1521278X-RAY DIFFRACTION96
3.9884-25.61190.19981450.18271296X-RAY DIFFRACTION92

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