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- PDB-5b1z: Crystal structure of Bcl-xL in complex with HBx-BH3 motif -

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Basic information

Entry
Database: PDB / ID: 5b1z
TitleCrystal structure of Bcl-xL in complex with HBx-BH3 motif
Components
  • Bcl-2-like protein 1
  • Peptide from Protein X
KeywordsAPOPTOSIS / HBx / Bcl-xL / HBV replication
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 / host cell mitochondrion / 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 / viral genome replication / 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 / defense response to virus / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / in utero embryonic development / mitochondrial inner membrane / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / host cell nucleus / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Transactivation protein X / Trans-activation protein 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 ...Transactivation protein X / Trans-activation protein 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 / 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
Protein X / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsYuan, Y.A.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology China
CitationJournal: To Be Published
Title: Crystal structure of Bcl-xL in complex with HBx-BH3 motif
Authors: Yuan, Y.A.
History
DepositionDec 22, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Peptide from Protein X
D: Peptide from Protein X


Theoretical massNumber of molelcules
Total (without water)40,5274
Polymers40,5274
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-54 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.708, 135.317, 97.593
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
11B-256-

HOH

21B-274-

HOH

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Components

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


Mass: 17506.504 Da / Num. of mol.: 2
Fragment: UNP residues 1-209, with deletion of residues 27-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide Peptide from Protein X / / HBx / Peptide X / pX


Mass: 2757.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Production host: Peptide display vector fth1 (others) / References: UniProt: I3XMW8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.07 Å3/Da / Density % sol: 40.45 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 1.05M Sodium Citrate, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 180 degree, 1 degree osillation
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 17371 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 22.4
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.974 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27388 944 5.2 %RANDOM
Rwork0.20509 ---
obs0.20852 17371 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--1.62 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2614 0 0 151 2765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192674
X-RAY DIFFRACTIONr_bond_other_d0.0020.022464
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.9223614
X-RAY DIFFRACTIONr_angle_other_deg0.89135632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50824.167144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6715446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0641518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02686
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_it0.8280.9841284
X-RAY DIFFRACTIONr_mcbond_other0.8280.9841283
X-RAY DIFFRACTIONr_mcangle_it1.3891.4651598
X-RAY DIFFRACTIONr_mcangle_other1.3881.4651599
X-RAY DIFFRACTIONr_scbond_it1.1331.0741388
X-RAY DIFFRACTIONr_scbond_other1.1331.0741389
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7811.5722016
X-RAY DIFFRACTIONr_long_range_B_refined4.3158.033288
X-RAY DIFFRACTIONr_long_range_B_other4.2847.8583259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 51 -
Rwork0.234 1108 -
obs--83.2 %
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)
12.7782-1.49060.30773.8855-1.35922.0140.07540.1666-0.2016-0.1302-0.324-0.19270.2130.32180.24860.07360.00150.00060.09650.05880.09669.906836.183636.6047
22.3148-1.0819-0.34653.04080.23791.51540.0137-0.05240.01830.0714-0.05370.0941-0.2139-0.04350.040.1033-0.0057-0.00030.0068-0.00420.0501-6.457854.876338.1727
34.96122.80031.70597.68560.49293.6753-0.270.3462-0.3919-0.96170.4316-0.08080.85170.2414-0.16150.4780.19650.10310.5050.11260.280519.798932.707825.7068
43.59444.77541.06410.56420.39661.6959-0.21250.33610.2691-0.74670.19340.8343-0.3529-0.1520.01910.38550.14010.01650.4173-0.07890.2444-19.184956.88830.004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 144
2X-RAY DIFFRACTION2B1 - 144
3X-RAY DIFFRACTION3C118 - 133
4X-RAY DIFFRACTION4D118 - 135

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