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- PDB-8xp5: The Crystal Structure of p53/BCL-xL fusion complex from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xp5
TitleThe Crystal Structure of p53/BCL-xL fusion complex from Biortus.
ComponentsBcl-2-like protein 1,Cellular tumor antigen p53
KeywordsPROTEIN BINDING / Apoptosis / Activator
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 / negative regulation of execution phase of apoptosis / fertilization / negative regulation of helicase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / Activation of NOXA and translocation to mitochondria / regulation of cell cycle G2/M phase transition / regulation of fibroblast apoptotic process / regulation of growth / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / regulation of mitochondrial membrane permeability / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / positive regulation of programmed necrotic cell death / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / glucose catabolic process to lactate via pyruvate / Bcl-2 family protein complex / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / NFE2L2 regulating tumorigenic genes / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / T cell lineage commitment / apoptotic mitochondrial changes / mitochondrial DNA repair / cellular response to alkaloid / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / ER overload response / B cell lineage commitment / hepatocyte apoptotic process / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / negative regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / TFIID-class transcription factor complex binding / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / rRNA transcription / negative regulation of anoikis / Transcriptional Regulation by VENTX / positive regulation of execution phase of apoptosis / replicative senescence / general transcription initiation factor binding / cellular response to UV-C / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
Similarity search - Function
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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 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 / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
Cellular tumor antigen p53 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of p53/BCL-xL fusion complex from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1,Cellular tumor antigen p53
B: Bcl-2-like protein 1,Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5424
Polymers83,4112
Non-polymers1312
Water2,054114
1
A: Bcl-2-like protein 1,Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7712
Polymers41,7061
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-4 kcal/mol
Surface area15800 Å2
MethodPISA
2
B: Bcl-2-like protein 1,Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7712
Polymers41,7061
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.976, 68.437, 77.055
Angle α, β, γ (deg.)90.000, 112.356, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bcl-2-like protein 1,Cellular tumor antigen p53 / Bcl2-L-1 / Apoptosis regulator Bcl-X / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 41705.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bcl-2-like protein 1/Cellular tumor antigen p53 fusion complex
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX, TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817, UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M MgCl2, 0.1M MES pH6.5, 5% PEG 4000, 10% 2-Propanol, 30% w/v D-Sorbito

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.55→49.36 Å / Num. obs: 20765 / % possible obs: 88.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 4.1
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.724 / Num. unique obs: 2602

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→49.36 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.811 / SU B: 21.431 / SU ML: 0.443 / Cross valid method: FREE R-VALUE / ESU R Free: 0.448
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3276 1042 5.024 %
Rwork0.2549 19699 -
all0.259 --
obs-20741 88.591 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.162 Å2
Baniso -1Baniso -2Baniso -3
1-1.193 Å2-0 Å2-4.688 Å2
2---0.789 Å20 Å2
3---2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 2 114 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164645
X-RAY DIFFRACTIONr_angle_refined_deg0.8251.6666843
X-RAY DIFFRACTIONr_angle_other_deg0.2741.57810675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.509543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48110833
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.032106
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.2710247
X-RAY DIFFRACTIONr_chiral_restr0.0360.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021234
X-RAY DIFFRACTIONr_nbd_refined0.2030.21099
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.24442
X-RAY DIFFRACTIONr_nbtor_refined0.1750.22460
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2161
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.224
X-RAY DIFFRACTIONr_nbd_other0.1360.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.213
X-RAY DIFFRACTIONr_mcbond_it1.3964.2382478
X-RAY DIFFRACTIONr_mcbond_other1.3954.2382478
X-RAY DIFFRACTIONr_mcangle_it2.5157.5953080
X-RAY DIFFRACTIONr_mcangle_other2.5157.5953081
X-RAY DIFFRACTIONr_scbond_it1.1054.3562575
X-RAY DIFFRACTIONr_scbond_other1.1054.3572576
X-RAY DIFFRACTIONr_scangle_it2.0397.9883763
X-RAY DIFFRACTIONr_scangle_other2.0397.9883764
X-RAY DIFFRACTIONr_lrange_it4.92943.995682
X-RAY DIFFRACTIONr_lrange_other4.92943.9985681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6160.367760.3521482X-RAY DIFFRACTION91.5932
2.616-2.6880.341690.3331428X-RAY DIFFRACTION91.1693
2.688-2.7650.404740.3291431X-RAY DIFFRACTION91.0466
2.765-2.850.416700.3071352X-RAY DIFFRACTION89.0977
2.85-2.9430.334750.261305X-RAY DIFFRACTION90.4325
2.943-3.0460.343760.2481258X-RAY DIFFRACTION90.2571
3.046-3.1610.412480.2571218X-RAY DIFFRACTION89.2807
3.161-3.2890.264490.251200X-RAY DIFFRACTION89.9856
3.289-3.4350.355770.2471111X-RAY DIFFRACTION89.1892
3.435-3.6010.358420.2511083X-RAY DIFFRACTION88.5827
3.601-3.7950.33570.2441005X-RAY DIFFRACTION88.3527
3.795-4.0240.31570.244963X-RAY DIFFRACTION88.4649
4.024-4.30.348500.224902X-RAY DIFFRACTION87.5
4.3-4.6410.278440.221820X-RAY DIFFRACTION86.4
4.641-5.080.289480.208734X-RAY DIFFRACTION85.8397
5.08-5.6720.271380.232685X-RAY DIFFRACTION84.3641
5.672-6.5350.341380.29584X-RAY DIFFRACTION83.6021
6.535-7.9690.262230.236509X-RAY DIFFRACTION83.5165
7.969-11.1260.337190.205397X-RAY DIFFRACTION81.7289
11.126-49.360.218120.271232X-RAY DIFFRACTION80.2632

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