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- PDB-8hlm: Crystal structure of p53/BCL2 fusion complex (complex 2) -

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Basic information

Entry
Database: PDB / ID: 8hlm
TitleCrystal structure of p53/BCL2 fusion complex (complex 2)
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 / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / 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 / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / metanephros development / neuron maturation / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / negative regulation of ossification / negative regulation of B cell apoptotic process / 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 / response to UV-B / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / regulation of mitochondrial membrane permeability / negative regulation of miRNA processing / response to iron ion / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / calcium ion transport into cytosol / mRNA transcription / bone marrow development / circadian behavior / channel activity / negative regulation of mitochondrial depolarization / histone deacetylase regulator activity / motor neuron apoptotic process / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / axon regeneration / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / epithelial cell apoptotic process / smooth muscle cell migration / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / organ growth / digestive tract 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 / 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 (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 / 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: 2.522 Å
AuthorsGuo, M. / Wang, H. / Wei, 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)41,6713
Polymers41,6052
Non-polymers651
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-2 kcal/mol
Surface area15990 Å2
Unit cell
Length a, b, c (Å)45.610, 70.336, 127.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 19502.291 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.: 4 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 0.1 M Imidazole, PEG8K 15-21% / PH range: 7.5-8.0

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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: 2.52→63.58 Å / Num. obs: 13872 / % possible obs: 96.21 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08788 / Net I/σ(I): 0.0935
Reflection shellResolution: 2.522→2.612 Å / Rmerge(I) obs: 0.9106 / Num. unique obs: 1383 / CC1/2: 0.924 / CC star: 0.98 / Rpim(I) all: 0.3083

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TUP/6QGG

1tup

6qgg


Resolution: 2.522→27.205 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2901 2549 9.98 %
Rwork0.2338 22994 -
obs0.2394 13839 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.68 Å2 / Biso mean: 87.9855 Å2 / Biso min: 47.75 Å2
Refinement stepCycle: final / Resolution: 2.522→27.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 1 4 2515
Biso mean--66.58 63.36 -
Num. residues----333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5224-2.57090.43351420.39561288100
2.5709-2.62330.39061460.39961363100
2.6233-2.68030.4387840.378776192
2.6803-2.74260.42631300.3675116892
2.7426-2.81120.36091490.3588133499
2.8112-2.88710.42841470.3318129898
2.8871-2.97190.40581470.3294127297
2.9719-3.06770.31921470.3064133899
3.0677-3.17720.38011400.27541311100
3.1772-3.30420.37471490.2886133399
3.3042-3.45430.32261480.27841304100
3.4543-3.6360.34391450.25691334100
3.636-3.86330.34491520.226132199
3.8633-4.16060.26621460.21451341100
4.1606-4.57750.20931460.18441316100
4.5775-5.23580.22971420.1812131299
5.2358-6.5810.2461450.2075129697
6.581-27.20.22531440.1657130498
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)
15.9426-0.0608-0.12657.10810.48188.98240.91740.34420.10690.569-0.6695-0.4534-0.6181.0894-0.45420.5912-0.03890.0810.61060.1050.58316.078539.531-19.0526
21.73390.6676-1.82657.12711.59325.87230.4612-0.13610.21660.4364-0.3005-0.2067-0.02530.2298-0.10280.5276-0.0250.06240.59920.03820.5852.557933.0292-11.0318
35.418103.02977.49581.21235.35460.01280.09910.50040.5128-0.3970.5986-0.666-0.09130.29220.69990.01490.10980.5149-0.04760.5843-4.635838.3095-9.5592
44.40372.1722-1.86263.92242.75326.73680.064-0.0034-0.54590.45330.4574-0.70791.51590.8491-0.27650.77460.1958-0.14410.5825-0.1780.72011.31531.3177-21.5293
53.7303-3.3925-1.87372.51842.24778.18090.3380.34010.37240.16030.3368-1.9148-0.90951.809-0.53360.60740.08550.03541.1518-0.31850.95977.970911.4025-28.5248
68.92241.6153-1.49816.32721.27546.5851-0.26131.3693-0.3655-0.00770.14040.5051.1572-1.28340.17830.6393-0.05410.02920.8025-0.10820.6184-13.05074.3052-22.524
77.97673.9174-3.92513.2111-3.51867.46441.1923-0.92721.43341.7479-0.87981.2541-1.397-0.5462-0.25370.9987-0.05560.1620.6453-0.09180.6914-12.655214.2853-9.7536
87.22776.6088-4.86139.3318-6.17315.67980.7262-0.35220.21981.93450.0433-0.146-1.57630.5289-0.66750.64270.25470.05040.5972-0.19020.7904-0.721317.9685-16.6684
95.05512.52140.47625.85341.42641.1247-0.3061-0.37390.9384-1.6275-0.26840.9703-0.7616-0.6280.75781.01930.36670.06921.08950.00460.7363-14.453515.2757-24.8718
106.83690.3305-0.78552.73291.0444.28990.1354-0.513-0.33930.20340.2992-1.20250.38111.1644-0.26410.37950.1169-0.08140.9801-0.16420.95885.928215.0665-24.4836
114.25571.8094-1.53952.43563.534910.16120.09720.1889-0.51180.61140.0044-0.4804-0.0142-0.4604-0.04320.5350.074-0.10680.5322-0.05970.7113-6.35346.3486-19.7544
121.5968-0.1303-2.6646.507-4.3716.4145-0.4370.2201-0.29010.39360.5594-0.24310.6737-1.28070.19850.82360.0415-0.07520.693-0.21710.79-2.85222.7759-25.2911
133.6468-0.5632-0.5670.0896-0.07630.3459-0.8240.4534-0.55812.63450.6131-0.27663.8171-0.04450.45152.51320.16580.04380.86830.19841.0022-0.4812-9.1866-10.9877
148.393-2.26240.56436.38082.01285.5674-0.511-0.5340.92151.21260.00490.1029-0.04040.48320.49550.9136-0.12690.0340.5949-0.02360.7587-0.447139.7719-1.5397
156.38443.25390.37767.6101-4.36963.27990.815-0.86150.56880.9583-0.7587-0.82330.2180.23330.29641.51430.1502-0.11980.79060.05970.91758.418240.8221.7847
163.08741.1851-0.9521.5485-0.91547.4524-0.3688-1.8754-1.71631.3140.71131.05361.26760.6671-0.14381.17490.07210.04580.78840.0940.9338-1.293627.5498-1.5658
172.16322.7894-0.567.55983.49726.7890.58021.7083-0.4078-1.48870.1104-0.71580.5320.6358-0.20290.73770.09960.03260.80630.03390.93578.467128.1435-16.2117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 119 through 137 )B119 - 137
2X-RAY DIFFRACTION2chain 'B' and (resid 138 through 164 )B138 - 164
3X-RAY DIFFRACTION3chain 'B' and (resid 165 through 202 )B165 - 202
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 140 )A95 - 140
5X-RAY DIFFRACTION5chain 'A' and (resid 141 through 155 )A141 - 155
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 176 )A156 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 194 )A177 - 194
8X-RAY DIFFRACTION8chain 'A' and (resid 195 through 203 )A195 - 203
9X-RAY DIFFRACTION9chain 'A' and (resid 204 through 213 )A204 - 213
10X-RAY DIFFRACTION10chain 'A' and (resid 214 through 229 )A214 - 229
11X-RAY DIFFRACTION11chain 'A' and (resid 230 through 263 )A230 - 263
12X-RAY DIFFRACTION12chain 'A' and (resid 264 through 274 )A264 - 274
13X-RAY DIFFRACTION13chain 'A' and (resid 275 through 288 )A275 - 288
14X-RAY DIFFRACTION14chain 'B' and (resid 7 through 25 )B7 - 25
15X-RAY DIFFRACTION15chain 'B' and (resid 26 through 90 )B26 - 90
16X-RAY DIFFRACTION16chain 'B' and (resid 91 through 107 )B91 - 107
17X-RAY DIFFRACTION17chain 'B' and (resid 108 through 118 )B108 - 118

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