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- PDB-5mcw: New Insights into the Role of DNA Shape on Its Recognition by p53... -

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Basic information

Entry
Database: PDB / ID: 5mcw
TitleNew Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LWC2)
Components
  • Cellular tumor antigen p53
  • DNA
KeywordsTRANSCRIPTION / P53 / TRANSCRIPTION FACTOR / DNA BINDING / DNA RECOGNITION / WATSON-CRICK BASE-PAIRING / INOSINE / 5-METHYLCYTOSINE / TRANSCRIPTION REGULATION / APOPTOSIS / BIOLOGICAL RHYTHMS / CELL CYCLE / NUCLEUS / TUMOR SUPPRESSOR / ANTIGEN NY-CO-13 / PHOSPHOPROTEIN
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / 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 ...negative regulation of helicase activity / signal transduction by p53 class mediator / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of cell cycle G2/M phase transition / 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 / oligodendrocyte apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / cellular response to actinomycin D / circadian behavior / positive regulation of programmed necrotic cell death / RUNX3 regulates CDKN1A transcription / 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 / Regulation of TP53 Activity through Association with Co-factors / Urea cycle / ER overload response / hematopoietic stem cell differentiation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 / TFIID-class transcription factor complex binding / replicative senescence / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Pyroptosis / determination of adult lifespan / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / negative regulation of fibroblast proliferation / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to glucose starvation / core promoter sequence-specific DNA binding / cis-regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Acetylation / intrinsic apoptotic signaling pathway / mitotic G1 DNA damage checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway / 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 / DNA damage response, signal transduction by p53 class mediator / protein phosphatase 2A binding / transcription initiation-coupled chromatin remodeling / molecular function activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / cellular response to ionizing radiation / cellular response to xenobiotic stimulus / TP53 Regulates Metabolic Genes / TP53 Regulates Transcription of DNA Repair Genes / cellular response to gamma radiation / Regulation of NF-kappa B signaling / mRNA 3'-UTR binding / protein tetramerization / promoter-specific chromatin binding / Stabilization of p53 / molecular condensate scaffold activity / negative regulation of cell growth / nucleotide-excision repair / G2/M Checkpoints / receptor tyrosine kinase binding / Autodegradation of the E3 ubiquitin ligase COP1 / cellular senescence / PML body / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / PKR-mediated signaling / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / transcription coactivator binding / positive regulation of reactive oxygen species metabolic process / intracellular protein localization / histone deacetylase binding
Similarity search - Function
Immunoglobulin-like - #720 / 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 ...Immunoglobulin-like - #720 / 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 / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMYL GROUP / DNA / DNA (> 10) / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.897 Å
AuthorsGolovenko, D. / Rozenberg, H. / Shakked, Z.
CitationJournal: Structure / Year: 2018
Title: New Insights into the Role of DNA Shape on Its Recognition by p53 Proteins.
Authors: Golovenko, D. / Brauning, B. / Vyas, P. / Haran, T.E. / Rozenberg, H. / Shakked, Z.
History
DepositionNov 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _struct.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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: Cellular tumor antigen p53
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6437
Polymers51,4523
Non-polymers1914
Water9,242513
1
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: DNA
hetero molecules

A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,28614
Polymers102,9056
Non-polymers3828
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.403, 68.408, 69.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 22505.582 Da / Num. of mol.: 2 / Fragment: P53 DNA BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: PET27-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637
#2: DNA chain DNA


Mass: 6441.137 Da / Num. of mol.: 1 / Fragment: DNA / Source method: obtained synthetically / Details: SYNTHESISED BY IDT / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Fragment: ZN / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 2 / Fragment: FORMYL / Source method: obtained synthetically / Formula: CH2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.92 % / Mosaicity: 0.149 °
Crystal growTemperature: 292 K / Method: evaporation / pH: 8.8
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane, 18% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.897→50 Å / Num. obs: 40479 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/av σ(I): 10.513 / Net I/σ(I): 3.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.897-1.935.20.3050.954175.7
1.93-1.9750.2880.954179.4
1.97-2.015.80.2820.952182.7
2.01-2.055.90.3020.933185.5
2.05-2.095.80.2670.955189.5
2.09-2.145.80.2610.95191.8
2.14-2.195.80.2530.956195
2.19-2.255.90.2410.947196.4
2.25-2.325.80.2250.967197.6
2.32-2.395.60.220.958198.3
2.39-2.486.50.2110.972199.6
2.48-2.586.60.1950.981199.9
2.58-2.76.60.1840.98199.8
2.7-2.846.60.1640.984199.8
2.84-3.026.30.1460.988198.8
3.02-3.256.20.1270.987199.6
3.25-3.586.70.1080.994199.9
3.58-4.096.40.1050.9911100
4.09-5.165.90.0960.99199.6
5.16-5060.0980.99199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.84 Å48.82 Å
Translation4.84 Å48.82 Å

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Processing

Software
NameVersionClassification
PHENIXdev-2276_1692refinement
PHASER2.5.7phasing
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TSR

1tsr


Resolution: 1.897→48.815 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.75
Details: Translational non-crystallographic symmetry (tNCS) correction
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 3085 7.67 %RANDOM SELECTION
Rwork0.1997 ---
obs0.2024 40244 93.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.54 Å2 / Biso mean: 21.5485 Å2 / Biso min: 3.99 Å2
Refinement stepCycle: final / Resolution: 1.897→48.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 410 6 513 4045
Biso mean--31.8 30.28 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063722
X-RAY DIFFRACTIONf_angle_d0.8675140
X-RAY DIFFRACTIONf_chiral_restr0.053558
X-RAY DIFFRACTIONf_plane_restr0.006611
X-RAY DIFFRACTIONf_dihedral_angle_d20.6142189
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8972-1.95850.29152290.26782640286975
1.9585-2.02850.27232400.2572946318683
2.0285-2.10970.27522640.23793159342389
2.1097-2.20570.28012850.23613367365294
2.2057-2.3220.29682860.22613470375697
2.322-2.46750.2512830.20893526380999
2.4675-2.6580.24722990.205935573856100
2.658-2.92540.22942940.20083570386499
2.9254-3.34860.23313010.187836003901100
3.3486-4.21860.1852970.163536483945100
4.2186-48.83140.20163070.16873676398396
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)
12.93540.1360.78930.8206-0.38710.64970.01580.2056-0.29350.01350.2093-0.24750.02070.2939-0.20820.11240.0086-0.02810.234-0.0530.1291139.27981.022612.8799
22.6472-0.35510.47250.4924-0.46360.8219-0.02070.2261-0.43640.03960.09-0.2640.120.1747-0.08570.13560.0243-0.03850.1438-0.06650.246136.862775.602812.826
30.6466-0.54210.15650.9282-0.2870.3624-0.12560.00640.0070.13040.121-0.0161-0.04890.00350.17410.1551-0.0117-0.0490.0614-0.01860.0495129.24489.378119.6349
40.963-0.6961.39882.24250.96924.2848-0.0846-0.6236-0.64440.37340.02410.29390.3028-0.3323-0.79730.17390.02350.00750.19040.12620.271118.692178.169925.5928
51.183-0.8697-0.74912.3748-0.35791.77310.0323-0.042-0.04670.56030.118-0.52050.07840.0466-0.12910.17310.0177-0.07820.1313-0.01130.2725131.692980.250628.6401
60.36220.468-0.2690.6173-0.43110.7086-0.05840.3274-0.5969-0.0411-0.0108-0.27390.25390.1293-0.0570.19720.0756-0.08740.2577-0.12410.4642142.663870.36721.6545
71.1827-0.24250.38050.6604-0.20910.9327-0.0083-0.03790.05910.0960.0863-0.0215-0.06930.0906-0.02640.06530.0005-0.04960.1443-0.03920.2573131.781782.27717.0089
84.09991.47370.35814.70050.74021.5333-0.07330.91720.2566-0.71580.26420.0679-0.0860.1465-0.11720.1845-0.0142-0.00660.3547-0.01060.1725128.006582.4019-2.9226
93.2846-0.45520.56470.7795-0.28770.90760.00040.4079-0.0879-0.08960.0828-0.3512-0.01460.2881-0.10520.14580.0183-0.00060.1660.01070.2488139.283646.828912.8845
102.11330.31460.42240.7715-0.21290.7605-0.05810.00150.0890.06620.1714-0.25320.02050.1009-0.02190.09680.0227-0.01690.1379-0.03370.1603132.297447.076316.1124
118.5163-0.83070.50031.6461.9632.6162-0.2047-0.7613-1.06350.4209-0.00490.2540.69-0.7384-0.12410.2329-0.03070.02810.27450.0360.2323120.025942.789126.638
120.3502-0.01520.16872.36550.34681.0704-0.0112-0.1418-0.07360.30120.1099-0.23030.0781-0.0120.17310.20190.01-0.07370.11090.02550.0775131.691646.055328.638
131.3890.45570.48320.3726-0.00761.1111-0.06190.1882-0.15750.09370.0523-0.13160.09270.1064-0.07550.16450.03-0.03080.0729-0.00330.0457134.4645.055718.1482
142.7318-0.94261.45643.44170.99871.5002-0.10530.75650.1993-0.55560.1134-0.3635-0.13740.2519-0.02850.1931-0.01930.01460.3254-0.02830.1307128.005248.1999-2.9467
150.4388-0.30090.09020.67890.11251.30870.07580.1813-0.0242-0.1932-0.01210.05410.084-0.04440.06050.1977-0.00750.00040.2187-0.01170.0276111.314486.20570.1141
162.8716-0.5910.10232.4363-0.25072.46890.14860.28040.0565-0.3287-0.0993-0.13190.1017-0.1698-0.1030.1586-0.02950.02440.16410.02590.3807111.321752.00090.1356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 94 through 123 )A94 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 155 )A124 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 176 )A156 - 176
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 194 )A177 - 194
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 213 )A195 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 229 )A214 - 229
7X-RAY DIFFRACTION7chain 'A' and (resid 230 through 277 )A230 - 277
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 292 )A278 - 292
9X-RAY DIFFRACTION9chain 'B' and (resid 94 through 123 )B94 - 123
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 180 )B124 - 180
11X-RAY DIFFRACTION11chain 'B' and (resid 181 through 194 )B181 - 194
12X-RAY DIFFRACTION12chain 'B' and (resid 195 through 213 )B195 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 214 through 277 )B214 - 277
14X-RAY DIFFRACTION14chain 'B' and (resid 278 through 292 )B278 - 292
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 10 )C1 - 10
16X-RAY DIFFRACTION16chain 'C' and (resid 11 through 20 )C11 - 20

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