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- PDB-6lhd: Crystal structure of p53/BCL-xL fusion complex -

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Basic information

Entry
Database: PDB / ID: 6lhd
TitleCrystal structure of p53/BCL-xL fusion complex
Componentsfusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
KeywordsPROTEIN BINDING / complex / interaction
Function / homology
Function and homology information


The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 ...The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / Transcriptional activation of cell cycle inhibitor p21 / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / regulation of mitochondrial membrane permeability / circadian behavior / cellular response to actinomycin D / apoptotic mitochondrial changes / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / Bcl-2 family protein complex / 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 / mRNA transcription / NFE2L2 regulating tumorigenic genes / Urea cycle / Regulation of TP53 Activity through Association with Co-factors / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / STAT5 activation downstream of FLT3 ITD mutants / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / entrainment of circadian clock by photoperiod / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / hematopoietic progenitor cell differentiation / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / 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 in response to DNA damage by p53 class mediator / Transcriptional Regulation by VENTX / replicative senescence / TFIID-class transcription factor complex binding / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway in absence of ligand / viral process / positive regulation of intrinsic apoptotic signaling pathway / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of fibroblast proliferation / general transcription initiation factor binding / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / response to cytokine / response to gamma radiation / 14-3-3 protein binding / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / regulation of mitochondrial membrane potential / negative regulation of autophagy / protein phosphatase 2A binding / molecular function activator activity / transcription initiation-coupled chromatin remodeling / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / regulation of cytokinesis / DNA damage response, signal transduction by p53 class mediator / TP53 Regulates Metabolic Genes / intrinsic apoptotic signaling pathway in response to DNA damage / autophagy
Similarity search - Function
Apoptosis regulator, Bcl-X / Immunoglobulin-like - #720 / 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 / Blc2-like ...Apoptosis regulator, Bcl-X / Immunoglobulin-like - #720 / 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 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / p53-like tetramerisation domain superfamily / 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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
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: 2.499 Å
AuthorsWei, H. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81372904, 81570537, 81974074 and 31900880 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural insight into the molecular mechanism of p53-mediated mitochondrial apoptosis.
Authors: Wei, H. / Qu, L. / Dai, S. / Li, Y. / Wang, H. / Feng, Y. / Chen, X. / Jiang, L. / Guo, M. / Li, J. / Chen, Z. / Chen, L. / Zhang, Y. / Chen, Y.
History
DepositionDec 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
B: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8504
Polymers83,7192
Non-polymers1312
Water1,892105
1
A: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9252
Polymers41,8601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9252
Polymers41,8601
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.221, 68.850, 75.028
Angle α, β, γ (deg.)90.000, 110.270, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein fusion protein of Bcl-2-like protein 1 and Isoform 6 of Cellular tumor antigen p53 / Bcl2-L-1 / Apoptosis regulator Bcl-X / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 41859.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCLX, 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.: 105 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium malonate pH 7.0, 20%(w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.499→50 Å / Num. obs: 23478 / % possible obs: 97 % / Redundancy: 3.4 % / CC1/2: 0.899 / Rmerge(I) obs: 0.1158 / Rrim(I) all: 0.1386 / Net I/σ(I): 7.89
Reflection shellResolution: 2.499→2.599 Å / Rmerge(I) obs: 0.6334 / Mean I/σ(I) obs: 2.46 / Num. unique obs: 2185 / CC1/2: 0.766 / Rrim(I) all: 0.7549

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMD, 2YXJ

3kmd

2yxj


Resolution: 2.499→49.217 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1210 5.16 %
Rwork0.2018 22237 -
obs0.2048 23447 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.58 Å2 / Biso mean: 58.2423 Å2 / Biso min: 18.78 Å2
Refinement stepCycle: final / Resolution: 2.499→49.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5007 0 2 105 5114
Biso mean--40.61 42.2 -
Num. residues----644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045123
X-RAY DIFFRACTIONf_angle_d0.5926954
X-RAY DIFFRACTIONf_chiral_restr0.043758
X-RAY DIFFRACTIONf_plane_restr0.004908
X-RAY DIFFRACTIONf_dihedral_angle_d8.4443043
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4995-2.59960.33451350.2617228992
2.5996-2.71790.29731430.2545244997
2.7179-2.86110.2631280.2352252599
2.8611-3.04040.34031360.2324249699
3.0404-3.27510.28081630.2148249799
3.2751-3.60460.30681290.2088239495
3.6046-4.12590.21981370.1915247297
4.1259-5.19730.21251050.1612573100
5.1973-49.20.23491340.1911254297
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)
12.1012-3.1659-1.82845.91354.14034.72140.37650.48940.7027-0.8199-0.4709-0.1882-0.621-0.12150.0630.42960.075-0.03730.4830.04350.428748.67518.308138.115
26.3229-0.058-5.90516.0643-1.67917.1228-0.8399-0.825-0.6191.4669-0.2585-0.0568-0.12570.08350.970.60950.1988-0.1050.7251-0.0090.705850.7998.617146.624
35.383-3.6766-2.30116.95144.60545.0709-0.8032-0.94930.33781.73341.0634-0.76040.1930.80210.01860.96570.1722-0.25990.74470.07050.878762.9989.166151.253
48.8509-5.0835-3.10065.87382.48733.588-0.3365-0.54170.4260.60230.3226-0.45570.38790.39450.00160.54560.057-0.1480.4034-0.02460.308457.64412.983142.875
58.5376-5.6150.23593.7194-0.24362.1763-0.4935-1.96190.55451.63320.5847-0.1573-0.30940.3937-0.31080.73790.0510.05221.0405-0.10890.649314.42417.87172.013
66.8992-0.2876-6.7110.75350.10977.8297-0.4878-2.14770.31180.50390.7320.1576-0.2682-0.2002-0.16250.58130.238-0.01711.49890.09490.63614.34513.578175.122
76.67661.3876-2.1182.0123-0.71682.26760.0451-0.7052-0.5113-0.22540.63880.60520.6327-0.1457-0.64090.90360.2068-0.25840.9171-0.00610.88593.3749.515161.932
86.27942.8855-5.59563.2659-1.89047.1478-0.4407-0.9101-0.6990.2589-0.1197-1.04690.04540.63290.48260.50230.1443-0.06940.75740.07880.6319.10510.991167.56
96.3691.9099-4.17747.3004-1.2937.5749-0.0919-0.03560.64850.2756-0.0020.5027-0.4631-0.9443-0.01870.50130.1126-0.07780.6574-0.03760.64869.49218.783161.258
103.06980.9759-1.99520.643-0.54241.86440.6694-0.29120.88510.68340.23320.8054-1.1289-1.3842-0.72410.84310.31580.35811.43470.04081.4674-3.30819.212178.63
111.6936-0.81741.46823.5996-0.78421.730.07750.14430.0154-0.051-0.0758-0.14270.06080.19370.01970.3994-0.0414-0.09030.2453-0.03730.326421.1624.469145.138
124.9183-1.04290.75353.4672-0.06833.09990.07860.126-0.23330.01590.00740.03130.0560.0801-0.07260.2872-0.0203-0.05720.1732-0.0070.191516.41-6.671142.769
137.5626-0.20330.14146.87094.60143.105-0.3033-0.4660.1198-0.5424-0.35181.91810.4054-1.08740.4770.6060.0126-0.19180.44360.01940.5987.52814.066136.423
142.451-0.0235-0.45864.1296-2.51271.75710.0909-0.25210.00360.725-0.04620.0747-0.4064-0.15810.13490.57670.0727-0.11170.2771-0.08910.392241.9659.996181.492
152.07140.36270.36215.33770.10081.7635-0.034-0.08520.27310.1031-0.0085-0.1403-0.08820.0490.02850.4058-0.0045-0.08530.2065-0.0280.2740.4055.751179.009
161.5277-0.7974-1.8612.47141.0577.379-0.1483-0.0795-0.11350.20240.10480.61550.6954-0.5504-0.08840.6119-0.1248-0.27980.40260.01270.65929.928-6.614171.209
173.05390.95152.67633.81243.76747.02160.55530.6849-0.4285-1.51620.16390.40120.70220.2825-0.67670.87330.1326-0.19390.44660.01910.470640.405-9.943167.913
189.1465-0.2867-1.36076.46061.79574.6710.0645-0.2413-0.36510.23610.00880.17080.08640.3118-0.04240.41740.0698-0.05550.1893-0.00070.208341.932-8.752178.35
195.28791.56153.78569.29492.9536.2685-0.07090.86130.43680.35840.2891-1.4502-0.46921.1066-0.22950.39960.0709-0.12560.417-0.01880.43152.2972.055181.948
202.76-0.17860.3454.499-0.63412.13970.15660.0028-0.0368-0.09720.02380.42730.3655-0.1636-0.19760.4843-0.0061-0.07520.1922-0.0260.278137.2082.128176.816
215.8639-5.5292-4.8415.93465.05454.8759-0.41850.2888-0.4639-0.7516-0.59262.2123-0.865-1.45110.6580.5331-0.0514-0.21220.60450.13140.596832.22519.106168.591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 3:44 )B3 - 44
2X-RAY DIFFRACTION2( CHAIN B AND RESID 45:81 )B45 - 81
3X-RAY DIFFRACTION3( CHAIN B AND RESID 82:96 )B82 - 96
4X-RAY DIFFRACTION4( CHAIN B AND RESID 97:155 )B97 - 155
5X-RAY DIFFRACTION5( CHAIN A AND RESID 3:20 )A3 - 20
6X-RAY DIFFRACTION6( CHAIN A AND RESID 21:58 )A21 - 58
7X-RAY DIFFRACTION7( CHAIN A AND RESID 59:96 )A59 - 96
8X-RAY DIFFRACTION8( CHAIN A AND RESID 97:116 )A97 - 116
9X-RAY DIFFRACTION9( CHAIN A AND RESID 117:136 )A117 - 136
10X-RAY DIFFRACTION10( CHAIN A AND RESID 137:149 )A137 - 149
11X-RAY DIFFRACTION11( CHAIN A AND RESID 162:221 )A162 - 221
12X-RAY DIFFRACTION12( CHAIN A AND RESID 222:341 )A222 - 341
13X-RAY DIFFRACTION13( CHAIN A AND RESID 342:355 )A342 - 355
14X-RAY DIFFRACTION14( CHAIN B AND RESID 163:189 )B163 - 189
15X-RAY DIFFRACTION15( CHAIN B AND RESID 190:234 )B190 - 234
16X-RAY DIFFRACTION16( CHAIN B AND RESID 235:246 )B235 - 246
17X-RAY DIFFRACTION17( CHAIN B AND RESID 247:260 )B247 - 260
18X-RAY DIFFRACTION18( CHAIN B AND RESID 261:279 )B261 - 279
19X-RAY DIFFRACTION19( CHAIN B AND RESID 280:295 )B280 - 295
20X-RAY DIFFRACTION20( CHAIN B AND RESID 296:343 )B296 - 343
21X-RAY DIFFRACTION21( CHAIN B AND RESID 344:355 )B344 - 355

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