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- PDB-8hln: Crystal structure of p53/BCL2 fusion complex(complex3) -

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Basic information

Entry
Database: PDB / ID: 8hln
TitleCrystal structure of p53/BCL2 fusion complex(complex3)
Components
  • Apoptosis regulator Bcl-2
  • Cellular tumor antigen p53
KeywordsAPOPTOSIS / Bcl-2 / p53
Function / homology
Function and homology information


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 / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / melanin metabolic process ...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 / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / 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 / BH domain binding / gland morphogenesis / renal system process / negative regulation of calcium ion transport into cytosol / regulation of cell-matrix adhesion / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / 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 / B cell apoptotic process / negative regulation of dendritic cell apoptotic process / negative regulation of T cell apoptotic process / regulation of nitrogen utilization / glomerulus development / metanephros development / positive regulation of multicellular organism growth / Regulation of MITF-M-dependent genes involved in apoptosis / focal adhesion assembly / negative regulation of motor neuron apoptotic process / neuron maturation / regulation of viral genome replication / oocyte development / endoplasmic reticulum calcium ion homeostasis / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / 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 / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / regulation of mitochondrial membrane permeability / positive regulation of mitochondrial membrane permeability / response to UV-B / negative regulation of ossification / positive regulation of programmed necrotic cell death / calcium ion transport into cytosol / negative regulation of mitophagy / mRNA transcription / circadian behavior / bone marrow development / response to iron ion / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of DNA damage response, signal transduction by p53 class mediator / RUNX3 regulates CDKN1A transcription / negative regulation of mitochondrial depolarization / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / motor neuron apoptotic process / axon regeneration / Activation of PUMA and translocation to mitochondria / epithelial cell apoptotic process / : / histone deacetylase regulator activity / smooth muscle cell migration / negative regulation of glial cell proliferation / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / organ growth / branching involved in ureteric bud morphogenesis / negative regulation of B cell apoptotic process / digestive tract morphogenesis
Similarity search - Function
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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...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 / 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 / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.354 Å
AuthorsGuo, M. / Wei, H. / Wang, H. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structures of p53/BCL-2 complex suggest a mechanism for p53 to antagonize BCL-2 activity.
Authors: Wei, H. / Wang, H. / Wang, G. / Qu, L. / Jiang, L. / Dai, S. / Chen, X. / Zhang, Y. / Chen, Z. / Li, Y. / Guo, M. / Chen, Y.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7853
Polymers41,7192
Non-polymers651
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-1 kcal/mol
Surface area16100 Å2
Unit cell
Length a, b, c (Å)44.701, 70.528, 127.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellular tumor antigen p53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22361.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637
#2: Protein Apoptosis regulator Bcl-2


Mass: 19358.162 Da / Num. of mol.: 1
Mutation: H20S,L95Q,R106L,F124G,R127Y,G128A,R129S,P168V,L175A,T178A,E179T,R183D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10415
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1 M HEPES, PEG8000 8%-13%, 0.8% ethylene glycol / PH range: 7.2-7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 16906 / % possible obs: 97.1 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.051 / Rrim(I) all: 0.177 / Χ2: 1.004 / Net I/σ(I): 7.8 / Num. measured all: 180047
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.397.30.6726730.9120.2250.7110.56981.3
2.39-2.437.40.7057610.9210.2360.7460.55587.8
2.43-2.487.80.6067810.9670.1950.6390.61891.9
2.48-2.538.30.6328040.9740.2020.6650.56794.6
2.53-2.598.80.5838220.9750.1830.6120.59996.1
2.59-2.659.40.6218350.9660.1930.6520.5897.3
2.65-2.71100.5838370.9740.1790.6110.63597.8
2.71-2.7910.30.5698540.9730.1720.5960.64198.6
2.79-2.8710.90.5098280.9750.1530.5320.70299.2
2.87-2.96110.3948560.9870.1190.4120.72599
2.96-3.0710.40.3358500.9870.1060.3520.82898.6
3.07-3.1911.10.2948810.9880.090.3080.922100
3.19-3.3311.50.2398450.9860.0720.251.13100
3.33-3.5111.80.1828590.9930.0550.1911.304100
3.51-3.73130.1628920.9940.0460.1691.33100
3.73-4.0213.10.1318610.9960.0380.1371.402100
4.02-4.42130.118940.9970.0310.1141.387100
4.42-5.0612.50.0988890.9970.0290.1021.524100
5.06-6.3711.60.0959210.9940.0290.11.348100
6.37-5011.80.0989630.9960.0290.1021.2499.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TUP/6QGG

1tup

6qgg


Resolution: 2.354→30.829 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 1681 10 %
Rwork0.2019 --
obs0.2071 16802 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.354→30.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 1 41 2663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032676
X-RAY DIFFRACTIONf_angle_d0.5413635
X-RAY DIFFRACTIONf_dihedral_angle_d9.5321577
X-RAY DIFFRACTIONf_chiral_restr0.041396
X-RAY DIFFRACTIONf_plane_restr0.003475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3544-2.42370.36151130.31381011X-RAY DIFFRACTION81
2.4237-2.50190.34771310.28111189X-RAY DIFFRACTION91
2.5019-2.59120.37121330.25571193X-RAY DIFFRACTION95
2.5912-2.69490.27821390.25681242X-RAY DIFFRACTION97
2.6949-2.81750.31071410.24791266X-RAY DIFFRACTION98
2.8175-2.96590.28251420.25041277X-RAY DIFFRACTION99
2.9659-3.15160.30451400.23531268X-RAY DIFFRACTION99
3.1516-3.39470.30541450.21951307X-RAY DIFFRACTION100
3.3947-3.73570.24911460.19261316X-RAY DIFFRACTION100
3.7357-4.27510.1921450.17621297X-RAY DIFFRACTION100
4.2751-5.38150.20921490.1531339X-RAY DIFFRACTION100
5.3815-30.80.21421570.17581416X-RAY DIFFRACTION100
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)
19.43242.7516-6.94987.0054-0.83068.7679-0.34870.26790.5870.16190.01231.11910.4168-0.39570.40480.452-0.0859-0.03270.6844-0.20910.4101-10.01244.0598-32.66
23.2539-0.05890.25667.107-4.46442.8242-0.3601-0.2576-0.28460.8288-0.147-0.8768-0.07050.83890.39350.53740.1169-0.11470.4888-0.12240.4127.42622.8936-21.1192
33.52710.828-0.07655.1907-0.30034.96460.16730.0592-0.33170.2328-0.0797-0.66740.39950.8527-0.08310.37220.1062-0.10290.4896-0.14170.37464.57215.4499-21.6567
44.49552.0088-1.37984.8475-0.30615.1949-0.08290.5361-0.36870.05940.00350.47230.6928-1.0633-0.08870.36060.01870.04280.481-0.07740.3624-12.6664.2735-22.5961
58.08896.3019-3.30566.3502-2.66636.45010.616-0.86711.13231.4257-0.36921.0945-0.6593-0.5262-0.49040.5914-0.00660.09050.3668-0.03630.3552-12.400614.3098-9.7911
63.77675.7754-1.49568.9779-1.45296.0037-0.17070.2153-0.23610.08580.6278-0.7552-0.69720.5879-0.21370.32820.05940.00770.3231-0.09250.3557-0.839318.2321-17.0624
78.48245.99363.78994.94764.46746.8131-0.35890.33920.8464-0.7051-0.05840.6243-0.6754-1.66520.32190.5150.29030.04640.81660.06530.4232-14.82115.1923-25.053
82.5198-0.30130.91773.4127-0.21113.815-0.39710.37550.13970.16880.3745-0.68110.02970.9461-0.01020.3444-0.0591-0.03720.4582-0.13040.33096.419715.9661-24.8038
94.41632.2483-2.57643.591-0.62958.3799-0.02190.2501-0.17190.37890.1444-0.24330.1775-0.423-0.16510.34030.108-0.04760.2833-0.05520.2302-5.19865.7724-21.3588
107.99674.14991.83435.92160.9062.0889-0.3961-0.8038-1.00240.4654-0.11230.1470.9718-0.01010.57211.19490.2159-0.01760.50930.00780.58171.4014-8.4224-11.4514
115.4154-0.93140.57888.68971.28398.53290.3066-0.42030.3588-0.0148-0.61880.1931-1.1493-0.80610.43660.6112-0.01850.05160.4726-0.07430.3562-0.797740.6315-1.4837
127.97912.09165.58254.6358-0.04154.75010.1812-1.18730.23280.2655-0.67810.26620.2895-1.22790.46850.91040.0165-0.00370.5533-0.00650.4854.148238.21834.7178
134.7937-5.0128-4.74697.28485.22624.93530.2923-0.9923-0.79451.0709-0.10290.04660.910.7479-0.27380.7105-0.0783-0.01760.4559-0.0410.5013-1.126327.6419-1.8025
146.57450.7799-0.30586.1444-2.39354.5618-0.03060.8975-0.173-0.5179-0.00060.02480.06860.29410.01770.4637-0.01930.02560.4236-0.02840.26354.664434.6234-18.3422
156.74072.51991.07625.075-0.17694.3584-0.11820.15020.07530.268-0.06320.0567-0.1806-0.11480.10450.41080.00740.04050.28360.01020.1778-1.258736.8096-9.3889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 91 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 203 )
7X-RAY DIFFRACTION7chain 'A' and (resid 204 through 213 )
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 229 )
9X-RAY DIFFRACTION9chain 'A' and (resid 230 through 274 )
10X-RAY DIFFRACTION10chain 'A' and (resid 275 through 288 )
11X-RAY DIFFRACTION11chain 'B' and (resid 7 through 24 )
12X-RAY DIFFRACTION12chain 'B' and (resid 25 through 91 )
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 107 )
14X-RAY DIFFRACTION14chain 'B' and (resid 108 through 143 )
15X-RAY DIFFRACTION15chain 'B' and (resid 144 through 203 )

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