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- PDB-8hll: Crystal structure of p53/BCL2 fusion complex (complex 1) -

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Basic information

Entry
Database: PDB / ID: 8hll
TitleCrystal structure of p53/BCL2 fusion complex (complex 1)
Components
  • Apoptosis regulator Bcl-2
  • Cellular tumor antigen p53
KeywordsAPOPTOSIS
Function / homology
Function and homology information


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 / channel inhibitor activity / melanin metabolic process ...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 / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / 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 / 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 / regulation of nitrogen utilization / negative regulation of dendritic cell apoptotic process / glomerulus development / focal adhesion assembly / regulation of transmembrane transporter activity / negative regulation of T cell apoptotic process / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / 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 / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-B / mRNA transcription / negative regulation of ossification / bone marrow development / positive regulation of programmed necrotic cell death / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / response to iron ion / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / epithelial cell apoptotic process / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / negative regulation of mitochondrial depolarization / axon regeneration / regulation of DNA damage response, signal transduction by p53 class mediator / motor neuron apoptotic process / positive regulation of smooth muscle cell migration / histone deacetylase regulator activity / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of B cell apoptotic process / negative regulation of neuroblast proliferation / organ growth / hair follicle morphogenesis / branching involved in ureteric bud 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 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 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 / 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: 2.62 Å
AuthorsWei, H. / Guo, M. / 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

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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)41,3833
Polymers41,3172
Non-polymers651
Water1086
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-3 kcal/mol
Surface area16010 Å2
Unit cell
Length a, b, c (Å)46.870, 70.480, 126.980
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: 22103.092 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: 19214.031 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: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.53 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: PEG 8K 8%-13%, 0.1M HEPES, 0.8% ethylene glycol / PH range: 7.4-7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.62→61.624 Å / Num. obs: 13228 / % possible obs: 99.74 % / Redundancy: 12.9 % / CC1/2: 0.977 / Rmerge(I) obs: 0.2568 / Rpim(I) all: 0.07537 / Rrim(I) all: 0.2679 / Net I/σ(I): 39.74
Reflection shellResolution: 2.62→2.714 Å / Redundancy: 13 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 1299 / CC1/2: 0.867 / CC star: 0.964 / Rpim(I) all: 0.3408 / % possible all: 99.85

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Processing

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

1tup

6qgg


Resolution: 2.62→61.624 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 2438 10.03 %
Rwork0.2246 --
obs0.2302 10864 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→61.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 1 6 2535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.553535
X-RAY DIFFRACTIONf_dihedral_angle_d7.0221526
X-RAY DIFFRACTIONf_chiral_restr0.041391
X-RAY DIFFRACTIONf_plane_restr0.003461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.67350.34651420.34741276X-RAY DIFFRACTION99
2.6735-2.73160.37661420.33641304X-RAY DIFFRACTION99
2.7316-2.79520.41971400.33131270X-RAY DIFFRACTION100
2.7952-2.86510.47371460.33321272X-RAY DIFFRACTION99
2.8651-2.94250.32651480.30761313X-RAY DIFFRACTION99
2.9425-3.02910.39451420.29581275X-RAY DIFFRACTION99
3.0291-3.12690.43121420.29681268X-RAY DIFFRACTION99
3.1269-3.23860.33381430.26091289X-RAY DIFFRACTION100
3.2386-3.36830.27441480.26031316X-RAY DIFFRACTION100
3.3683-3.52160.32391370.24891294X-RAY DIFFRACTION100
3.5216-3.70720.33551450.22791279X-RAY DIFFRACTION100
3.7072-3.93950.22531470.21871296X-RAY DIFFRACTION100
3.9395-4.24360.25051460.1911307X-RAY DIFFRACTION100
4.2436-4.67050.19681370.16531284X-RAY DIFFRACTION100
4.6705-5.3460.20561450.16251271X-RAY DIFFRACTION100
5.346-6.7340.22291470.19991295X-RAY DIFFRACTION100
6.734-61.60.27231410.19561268X-RAY DIFFRACTION98
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)
17.21210.259-1.29727.51582.47057.5959-0.20110.9216-0.302-0.86520.5271-0.33640.286-0.0392-0.43170.5293-0.1812-0.0190.6179-0.07050.3147-1.58125.0403-33.5777
25.3256-1.0419-2.84511.75791.65113.0849-0.033-0.8971-0.70141.64870.0497-0.87681.83630.9299-0.13171.14390.2572-0.38060.6258-0.08710.74212.5554-1.1077-13.6103
35.6342-3.612-1.96244.67023.04966.95010.34130.25820.0195-0.34120.0832-1.6667-0.54211.8289-0.4560.2948-0.0107-0.03030.6338-0.24220.6347.92611.4485-28.3768
45.97390.49030.03645.99320.79584.77770.02760.7460.2030.13930.04271.04021.6021-1.5646-0.06030.4389-0.1528-0.03020.7703-0.0620.351-13.23074.7592-22.6926
57.48645.9008-4.01366.1265-5.27215.03651.2203-1.58231.00661.236-0.54481.3789-1.7382-1.0298-0.65540.5773-0.04750.0860.69070.01330.5102-12.78814.6286-9.6925
65.8253.80161.22487.11213.0247.4332-0.44720.0919-0.0978-0.9460.5039-0.0021-1.4155-0.87860.03680.44860.16980.02650.4551-0.00810.3427-8.242916.8706-21.236
70.8765-0.7988-0.03340.76090.38614.34230.09550.2769-0.8050.33990.4515-1.1676-0.21050.7048-0.24230.342-0.1276-0.03230.5987-0.2130.8546.337915.1349-24.4571
82.64721.2839-0.99424.34732.38667.62430.09330.0769-0.36370.62430.2588-0.07381.1883-0.7451-0.19390.46-0.037-0.01990.4684-0.00910.3795-6.43266.7771-20.0167
94.31711.1935-1.31814.65632.35382.06530.1865-0.4892-1.15960.9292-0.1932-0.32592.41410.91730.09931.0990.0362-0.22530.4682-0.06590.641-2.2201-3.0483-18.2391
102.0914-2.0535-3.03257.77391.63954.7851-0.3581-0.1999-0.39981.647-0.14980.6975-0.3461-0.3890.23610.94530.11340.04360.6019-0.06820.4341-0.261739.9219-1.2702
118.10994.8439-4.49762.985-2.03418.5997-0.0288-1.7351-0.41840.7126-0.52081.2987-2.02361.4911-0.08531.15070.0743-0.1770.637-0.09150.78898.37540.77372.0608
129.7921-1.378-2.50829.13120.27822.3671-0.2283-0.4895-0.72361.02550.2760.05561.25910.20380.03380.63190.0425-0.11680.46630.04260.45752.580928.0483-7.0075
133.96621.52271.59748.7667-0.33037.99190.00630.18360.43990.2333-0.1327-0.06-0.69240.52620.13470.4122-0.00480.03640.35250.03390.35353.698138.2997-13.1957
144.69591.47142.62389.23481.48091.59421.0387-1.57520.40082.278-0.35581.5623-0.3559-0.9037-0.08860.39750.04460.37160.7793-0.23110.9384-13.668432.3203-7.6562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 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 213 )
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 229 )
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 263 )
9X-RAY DIFFRACTION9chain 'A' and (resid 264 through 288 )
10X-RAY DIFFRACTION10chain 'B' and (resid 7 through 25 )
11X-RAY DIFFRACTION11chain 'B' and (resid 26 through 90 )
12X-RAY DIFFRACTION12chain 'B' and (resid 91 through 118 )
13X-RAY DIFFRACTION13chain 'B' and (resid 119 through 184 )
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 202 )

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