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- PDB-5fcg: Crystal structure of Bcl-2 in complex with HBx-BH3 motif -

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Basic information

Entry
Database: PDB / ID: 5fcg
TitleCrystal structure of Bcl-2 in complex with HBx-BH3 motif
Components
  • Apoptosis regulator Bcl-2
  • Protein X
KeywordsAPOPTOSIS / Complex
Function / homology
Function and homology information


symbiont-mediated activation of host NF-kappaB cascade / channel inhibitor activity / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / symbiont-mediated perturbation of host cell cycle progression / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process ...symbiont-mediated activation of host NF-kappaB cascade / channel inhibitor activity / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / symbiont-mediated perturbation of host cell cycle progression / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / symbiont-mediated arrest of host cell cycle during G2/M transition / positive regulation of melanocyte differentiation / melanin metabolic process / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / negative regulation of calcium ion transport into cytosol / stem cell development / lymphoid progenitor cell differentiation / T cell apoptotic process / melanocyte differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial 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 T cell apoptotic process / B cell apoptotic process / glomerulus development / regulation of nitrogen utilization / positive regulation of multicellular organism growth / metanephros development / Regulation of MITF-M-dependent genes involved in apoptosis / neuron maturation / focal adhesion assembly / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / oocyte development / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / response to UV-B / calcium ion transport into cytosol / response to iron ion / negative regulation of ossification / motor neuron apoptotic process / negative regulation of mitochondrial depolarization / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / negative regulation of B cell apoptotic process / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / digestive tract morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / positive regulation of smooth muscle cell migration / negative regulation of G1/S transition of mitotic cell cycle / pore complex / negative regulation of intrinsic apoptotic signaling pathway / T cell homeostasis / BH3 domain binding / B cell homeostasis / humoral immune response / B cell proliferation / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / regulation of calcium ion transport / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hematopoietic stem cell differentiation / host cell mitochondrion / behavioral fear response / response to glucocorticoid / cellular response to glucose starvation / ovarian follicle development / skeletal muscle fiber development / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / homeostasis of number of cells within a tissue / positive regulation of B cell proliferation / response to cytokine / negative regulation of autophagy / regulation of transmembrane transporter activity / reactive oxygen species metabolic process / axonogenesis
Similarity search - Function
Transactivation protein X / Trans-activation protein X / Apoptosis regulator, Bcl-2 / 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-2 / 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
Protein X / Apoptosis regulator Bcl-2 / Protein X
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJiang, T.Y. / Liu, M.H. / Wu, J.P. / Shi, Y.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural and biochemical analysis of Bcl-2 interaction with the hepatitis B virus protein HBx
Authors: Jiang, T.Y. / Liu, M.H. / Wu, J.P. / Shi, Y.G.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references / Other
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2
C: Protein X


Theoretical massNumber of molelcules
Total (without water)22,6032
Polymers22,6032
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-12 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.777, 82.990, 33.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 19440.623 Da / Num. of mol.: 1 / Mutation: ALA36 mutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P10415*PLUS
#2: Protein/peptide Protein X / HBx / Peptide X / pX


Mass: 3162.652 Da / Num. of mol.: 1 / Fragment: UNP residues 110-135 / Source method: obtained synthetically / Source: (synth.) Hepatitis B virus / References: UniProt: E9L5H4, UniProt: Q99HR6*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REFERENCE SEQUENCE DATABASE FOR CHAIN A DOES NOT CURRENTLY EXIST. RESIDUE ALA A 36 IS MUTATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.08 % / Description: neddle
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100mM sodium acetate, 500mM ammonium sulfate / PH range: 4.6 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 10943 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 17.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XA0

2xa0


Resolution: 2.1→34.781 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 518 4.79 %
Rwork0.2552 --
obs0.2562 10804 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 0 93 1547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0211503
X-RAY DIFFRACTIONf_angle_d2.0372030
X-RAY DIFFRACTIONf_dihedral_angle_d19.222541
X-RAY DIFFRACTIONf_chiral_restr0.143207
X-RAY DIFFRACTIONf_plane_restr0.009264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0986-2.30970.38141370.3522411X-RAY DIFFRACTION96
2.3097-2.64380.32931170.26582568X-RAY DIFFRACTION100
2.6438-3.33060.28051300.25712598X-RAY DIFFRACTION100
3.3306-34.7860.22441340.22142709X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 75.2023 Å / Origin y: 181.2699 Å / Origin z: 3.068 Å
111213212223313233
T0.1293 Å2-0.0079 Å20.0197 Å2-0.142 Å2-0.0066 Å2--0.1016 Å2
L1.8013 °20.0988 °20.2004 °2-2.2666 °2-0.215 °2--1.2659 °2
S-0.0203 Å °-0.0634 Å °0.0595 Å °0.0364 Å °-0.0187 Å °-0.0202 Å °-0.0281 Å °0.0275 Å °0.033 Å °
Refinement TLS groupSelection details: all

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