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

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Basic information

Entry
Database: PDB / ID: 5mcv
TitleNew Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LWC1)
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 / Association of TriC/CCT with target proteins during biosynthesis / hematopoietic progenitor cell differentiation / 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 / replicative senescence / Transcriptional Regulation by VENTX / TFIID-class transcription factor complex binding / 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 / 14-3-3 protein binding / response to gamma radiation / MDM2/MDM4 family protein binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / protein phosphatase 2A binding / DNA damage response, signal transduction by p53 class mediator / 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 / mRNA 3'-UTR binding / Regulation of NF-kappa B signaling / protein tetramerization / molecular condensate scaffold activity / promoter-specific chromatin binding / Stabilization of p53 / 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 / PKR-mediated signaling / positive regulation of miRNA transcription / Oncogene Induced Senescence / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / intracellular protein localization / positive regulation of reactive oxygen species metabolic process / 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
ACETATE ION / 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: 1.6 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)52,32217
Polymers51,4523
Non-polymers87014
Water10,359575
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)104,64434
Polymers102,9056
Non-polymers1,73928
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
MethodPISA
Unit cell
Length a, b, c (Å)138.078, 49.533, 68.047
Angle α, β, γ (deg.)90.000, 92.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / DNA chain , 2 types, 3 molecules ABC

#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)

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Non-polymers , 4 types, 589 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Fragment: ACETATE ION / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.29 Å3/Da / Density % sol: 46.22 % / Mosaicity: 0.403 °
Crystal growTemperature: 292 K / Method: evaporation / pH: 8.8
Details: 0.02 M Citric acid, 0.08 M BIS-TRIS propane, 16% 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: 1.6→35 Å / Num. obs: 60494 / % possible obs: 99.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 14.48 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.033 / Rrim(I) all: 0.08 / Χ2: 1.008 / Net I/av σ(I): 24.279 / Net I/σ(I): 5.2 / Num. measured all: 346296
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.634.30.39429690.940.2090.4480.96497.5
1.63-1.665.20.37630090.9670.180.4180.97399.6
1.66-1.695.50.31230070.9740.1440.3440.96899.7
1.69-1.725.70.29529900.9810.1350.3250.96799.6
1.72-1.765.80.25529950.9850.1150.2810.98699.5
1.76-1.85.80.22830190.990.1020.2510.98499.4
1.8-1.855.80.21130400.9890.0950.2321.01499.3
1.85-1.95.60.17429770.9910.0790.1921.00799.2
1.9-1.955.20.15129770.9930.0720.1681.05798.9
1.95-2.025.90.13530250.9950.060.1481.0299.8
2.02-2.096.10.12130220.9960.0530.1321.02599.6
2.09-2.176.10.10430320.9960.0460.1141.00199.6
2.17-2.276.10.09230580.9970.0410.1011.00599.3
2.27-2.395.90.08429780.9970.0370.0921.01699.3
2.39-2.545.30.07930340.9960.0370.0881.00899.2
2.54-2.746.20.07130730.9980.0310.0771.01699.8
2.74-3.016.20.06330180.9980.0280.0691.00399.8
3.01-3.455.90.05430530.9980.0240.0591.03999.3
3.45-4.345.70.04630590.9980.0210.0511.04299.3
4.34-355.90.04531590.9990.020.0491.03599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.6 Å34.48 Å
Translation1.6 Å34.48 Å

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Processing

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

1tsr


Resolution: 1.6→34.475 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 3007 4.99 %RANDOM SELECTION
Rwork0.1541 57222 --
obs0.1558 60229 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.29 Å2 / Biso mean: 20.4157 Å2 / Biso min: 3.24 Å2
Refinement stepCycle: final / Resolution: 1.6→34.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3111 410 50 575 4146
Biso mean--29.07 33.35 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063906
X-RAY DIFFRACTIONf_angle_d0.9685391
X-RAY DIFFRACTIONf_chiral_restr0.058583
X-RAY DIFFRACTIONf_plane_restr0.005644
X-RAY DIFFRACTIONf_dihedral_angle_d14.4872344
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 (%)
1.5996-1.65120.26552670.23755131539898
1.6512-1.71020.26662660.2135171543799
1.7102-1.77870.24272750.19935172544799
1.7787-1.85960.22352810.18255161544299
1.8596-1.95770.21882740.17185175544999
1.9577-2.08030.19082680.159152355503100
2.0803-2.24090.18872680.15075195546399
2.2409-2.46640.17352710.14645224549599
2.4664-2.82310.1822800.14225252553299
2.8231-3.55620.16762710.13925251552299
3.5562-34.48310.16082860.13065255554197
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)
10.0458-0.0130.00530.0134-0.01880.0793-0.0851-0.02190.09990.07310.0091-0.12880.02940.0051-0.22150.09560.0785-0.00330.10020.06630.176166.690314.691287.666
20.0030.0093-0.00320.0228-0.00980.00230.02850.14360.189-0.1447-0.06090.0883-0.1139-0.1329-0.00790.14580.05580.00990.20530.03320.2208152.287328.518672.3337
30.1529-0.19180.06920.2637-0.09230.03440.05450.22210.0923-0.1411-0.122-0.0856-0.0049-0.0239-0.110.07910.0136-0.01070.1032-0.01140.1282159.70519.616176.7133
40.1994-0.0728-0.00320.1227-0.01150.0061-0.0501-0.0958-0.12040.0345-0.00870.0701-0.0045-0.0911-0.07490.05760.01340.02420.0935-0.00370.064151.927111.911289.6453
50.01010.00860.0410.2790.05170.14940.06030.116-0.0752-0.1556-0.09930.15260.0526-0.07140.11450.05790.0366-0.08260.1164-0.08660.0169147.19036.266175.848
60.3762-0.00580.08710.53610.09080.4685-0.04370.0526-0.0173-0.02950.02710.0110.0998-0.050.00630.07950.0102-0.00240.0699-0.0190.0261156.49212.338981.6655
70.02720.00890.00020.01640.0070.00220.0620.02510.0565-0.1041-0.03990.1304-0.01710.00250.00030.13510.0094-0.0320.11210.03590.19150.296435.244483.6119
80.3565-0.1379-0.00130.5177-0.22930.1223-0.1006-0.08490.06150.1570.0292-0.13250.0335-0.0613-0.13680.1267-0.0306-0.02260.1264-0.04050.0527168.419414.692653.6875
90.04320.09990.10110.22730.22890.2345-0.00220.12550.1393-0.1944-0.09960.1283-0.0548-0.1132-0.0680.25280.0502-0.08130.19410.08040.2171154.011728.518138.3499
100.39760.09410.14130.3379-0.05090.1299-0.01720.1292-0.0099-0.0389-0.0149-0.0461-0.03280.0234-0.07110.090800.00290.09670.02120.0438161.339519.68642.6925
110.5509-0.2424-0.02560.22850.11380.1046-0.0981-0.1163-0.15530.09360.02570.11150.0018-0.0143-0.15670.08390.01420.01530.05150.00890.0619153.670312.02155.8175
120.5734-0.2001-0.06021.49610.02640.36040.01810.1049-0.1523-0.1394-0.0480.50420.111-0.16510.05450.147-0.03510.00790.0708-0.00040.1292148.80086.34741.9203
130.26640.01550.25540.58930.16030.3202-0.0229-0.00320.07210.0802-0.0069-0.0221-0.0140.0475-0.06280.05320.0120.0120.05740.02780.0974158.166612.24447.7178
140.02450.0018-0.00120.01880.00880.0030.05270.01580.0699-0.1298-0.0630.13320.01910.01380.00020.1343-0.0023-0.00780.1078-0.01580.178152.027335.243549.6422
150.02810.02050.02090.02540.02670.02380.2098-0.19060.09570.1013-0.0901-0.09350.0423-0.00490.00020.2156-0.01630.01960.1423-0.04620.1486134.181934.86192.2921
160.0089-0.0803-0.00990.72590.08730.01060.14150.23-0.1703-0.35420.1049-0.03930.0066-0.13880.05720.19470.0913-0.10960.2222-0.0080.2056132.83528.292275.0343
170.06740.01780.00160.03320.04840.07170.1694-0.130.06750.12790.0051-0.083-0.04940.00080.00550.135-0.04930.03020.2077-0.05610.1371135.910234.857158.3119
180.0288-0.0228-0.0150.03140.02670.02430.19510.2387-0.248-0.46790.054-0.0479-0.0913-0.19110.00030.2403-0.0346-0.01580.24040.04770.1722134.56628.288341.0594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 94 through 112 )A94 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 123 )A113 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 155 )A124 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 176 )A156 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 203 )A177 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 277 )A204 - 277
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 293 )A278 - 293
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 112 )B94 - 112
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 123 )B113 - 123
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 155)B124 - 155
11X-RAY DIFFRACTION11chain 'B' and (resid 156 through 176 )B156 - 176
12X-RAY DIFFRACTION12chain 'B' and (resid 177 through 203 )B177 - 203
13X-RAY DIFFRACTION13chain 'B' and (resid 204 through 277 )B204 - 277
14X-RAY DIFFRACTION14chain 'B' and (resid 278 through 293)B278 - 293
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 6 )C1 - 6
16X-RAY DIFFRACTION16chain 'C' and (resid 7 through 10 )C7 - 10
17X-RAY DIFFRACTION17chain 'C' and (resid 11 through 16 )C11 - 16
18X-RAY DIFFRACTION18chain 'C' and (resid 17 through 20 )C17 - 20

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