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

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Basic information

Entry
Database: PDB / ID: 5mcu
TitleNew Insights into the Role of DNA Shape on Its Recognition by p53 Proteins (complex p53DBD-LHG2)
Components
  • Cellular tumor antigen p53
  • DNA
KeywordsTRANSCRIPTION / P53 / TRANSCRIPTION FACTOR / DNA BINDING / DNA RECOGNITION / HOOGSTEEN BASE-PAIRING / ISOGUANINE / 2-OXO-ADENINE / 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 / 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 ...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 / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / mRNA transcription / 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 / germ cell nucleus / RUNX3 regulates CDKN1A transcription / glucose catabolic process to lactate via pyruvate / 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 / regulation of DNA damage response, signal transduction by p53 class mediator / histone deacetylase regulator activity / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / thymocyte apoptotic process / B cell lineage commitment / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / negative regulation of mitophagy / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / 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 by p53 class mediator / rRNA transcription / negative regulation of reactive oxygen species metabolic process / Transcriptional Regulation by VENTX / cellular response to UV-C / replicative senescence / general transcription initiation factor binding / cellular response to actinomycin D / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of RNA polymerase II transcription preinitiation complex assembly / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of execution phase of apoptosis / viral process / Pyroptosis / hematopoietic stem cell differentiation / response to X-ray / embryonic organ development / chromosome organization / type II interferon-mediated signaling pathway / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / glial cell proliferation / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / mitophagy / cis-regulatory region sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / Regulation of TP53 Activity through Acetylation / gastrulation / response to salt stress / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / negative regulation of proteolysis / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex / intrinsic apoptotic signaling pathway
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 / 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
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: 1.7 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)51,98811
Polymers51,4843
Non-polymers5038
Water7,782432
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)103,97522
Polymers102,9696
Non-polymers1,00616
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.133, 68.422, 69.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-175-

HOH

21C-176-

HOH

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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: 6473.133 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Fragment: 1,2-ETHANEDIOL / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.52 Å3/Da / Density % sol: 51.14 % / Mosaicity: 0.355 °
Crystal growTemperature: 292 K / Method: evaporation / pH: 7
Details: 0.05 M HEPES sodium salt, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 57404 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 17.02 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/av σ(I): 16.807 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.7-1.7330.3970.945199
1.73-1.763.10.4050.903199.2
1.76-1.793.10.3520.925199.4
1.79-1.833.10.3320.929199.4
1.83-1.873.10.2910.943199
1.87-1.9130.2610.95196.8
1.91-1.963.30.2240.965199.4
1.96-2.023.40.2020.971199.3
2.02-2.073.40.1840.975199.5
2.07-2.145.40.2560.981199.6
2.14-2.226.80.2520.986199.7
2.22-2.316.40.2210.986199.3
2.31-2.417.40.1980.99199.7
2.41-2.547.30.1760.992199.8
2.54-2.77.30.1510.994199.8
2.7-2.9170.1310.99199.7
2.91-3.27.20.1020.997199.7
3.2-3.667.60.0860.996199.3
3.66-4.6170.0730.996199.1
4.61-507.40.0710.997198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.8 Å48.74 Å
Translation4.8 Å48.74 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: PDBID 1TSR

1tsr


Resolution: 1.7→42.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.58
Details: Translational non-crystallographic symmetry (tNCS) correction
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2975 5.21 %RANDOM SELECTION
Rwork0.1688 ---
obs0.1704 57096 98.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.14 Å2 / Biso mean: 24.405 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 1.7→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 412 26 432 3887
Biso mean--25.03 35.65 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073759
X-RAY DIFFRACTIONf_angle_d0.8675190
X-RAY DIFFRACTIONf_chiral_restr0.055567
X-RAY DIFFRACTIONf_plane_restr0.006616
X-RAY DIFFRACTIONf_dihedral_angle_d18.0062243
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 (%)
1.6997-1.75460.28892600.24374686494696
1.7546-1.81730.24242790.22464882516199
1.8173-1.89010.22182640.20984865512999
1.8901-1.97610.20422580.18994873513198
1.9761-2.08030.22162730.17984906517999
2.0803-2.21060.22482660.172249405206100
2.2106-2.38130.21012760.16544937521399
2.3813-2.62090.18292710.163449595230100
2.6209-3.00010.19052760.1544985526199
3.0001-3.77940.16812720.14265012528499
3.7794-42.91410.19552800.16015076535696
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)
10.0643-0.0054-0.02370.00060.00260.2914-0.1573-0.29290.2603-0.03560.23710.0542-0.4357-0.30950.00780.2863-0.028-0.03760.39810.03120.5004131.945122.1047-19.3162
20.61780.19040.15840.383-0.09120.09860.0399-0.1529-0.2653-0.00320.08480.02560.1049-0.2130.09880.0857-0.0301-0.00540.18630.02850.171139.8996108.4604-11.0106
30.3878-0.08910.02560.2653-0.00430.226-0.06260.03740.0915-0.07110.0986-0.029-0.0167-0.02130.01760.19360.0045-0.0460.1564-0.01220.0926145.958123.1467-19.6863
40.1124-0.04140.13220.0204-0.02510.259-0.01210.2336-0.3759-0.23710.1221-0.09780.18430.20060.02270.24190.0055-0.02340.2015-0.06990.2283152.3272109.9978-25.8278
50.04840.0176-0.0150.0413-0.00920.07010.0310.1776-0.0089-0.3069-0.18790.1768-0.35310.087-0.00680.3676-0.03-0.08210.1983-0.02190.1932143.5836121.0646-31.4844
60.284-0.32130.36940.4211-0.2580.9450.0076-0.012-0.0975-0.10090.0140.03250.0864-0.14580.04520.1385-0.0099-0.01440.09030.00820.0926141.9829114.2093-18.1846
70.24240.1236-0.28650.124-0.11810.35220.0763-0.20710.10910.08220.03680.1069-0.0462-0.14320.09760.1254-0.01580.04330.25190.01450.1177147.3384115.94762.5676
80.26850.20110.34310.27410.50560.9398-0.1631-0.36050.1375-0.01540.13270.0444-0.2624-0.41850.130.20330.0264-0.06190.27270.08920.2721131.9438156.3121-19.3046
90.7576-0.16580.3630.3112-0.28720.3280.0148-0.1518-0.2277-0.04010.09570.10150.1031-0.23090.04570.1334-0.042-0.03090.1650.03710.1201139.9007142.6692-11.0134
100.51020.21020.45450.15250.44811.4551-0.11680.01110.1664-0.218-0.0017-0.0153-0.2476-0.0404-0.3640.1345-0.03030.01890.09130.05140.1832145.9607157.3613-19.6861
110.2777-0.02720.27330.016-0.01090.28740.0410.2504-0.351-0.24040.1023-0.10250.12990.21670.00270.2159-0.00990.00390.193-0.0240.2096152.3417144.2013-25.8385
120.3095-0.304-0.01960.7361-0.13010.0525-0.02910.06510.0316-0.2936-0.05410.0694-0.22710.0727-0.1780.2779-0.0324-0.0380.09870.02820.1025143.5893155.2702-31.4722
130.1919-0.29820.20480.493-0.26810.9756-0.0027-0.1129-0.1235-0.08090.0876-0.01610.0584-0.09290.01290.1252-0.0389-0.0190.17770.01070.1734142.0906148.3636-18.0969
140.0962-0.04070.00180.0375-0.05080.12620.2489-0.23870.0046-0.0282-0.1001-0.0484-0.0394-0.24630.00540.1826-0.024-0.00610.2540.01870.1681147.343150.15952.5659
150.43890.2462-0.17620.1376-0.09870.35070.1294-0.06420.00350.1198-0.00620.03110.0369-0.02130.00470.19490.0012-0.0420.1657-0.02240.1323163.9847154.4717-0.057
160.59770.3298-0.1220.5634-0.12210.34190.07130.02370.06950.1517-0.09990.0042-0.0332-0.06870.01450.1047-0.00220.05750.12070.0010.1701163.9828120.2566-0.0558
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 109 )A95 - 109
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 155 )A110 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 176 )A156 - 176
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 203 )A177 - 203
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 213 )A204 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 277 )A214 - 277
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 291 )A278 - 291
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 109 )B95 - 109
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 155 )B110 - 155
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 176 )B156 - 176
11X-RAY DIFFRACTION11chain 'B' and (resid 177 through 203 )B177 - 203
12X-RAY DIFFRACTION12chain 'B' and (resid 204 through 213 )B204 - 213
13X-RAY DIFFRACTION13chain 'B' and (resid 214 through 277 )B214 - 277
14X-RAY DIFFRACTION14chain 'B' and (resid 278 through 291 )B278 - 291
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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