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- PDB-4iby: Human p53 core domain with hot spot mutation R273H and second-sit... -

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Basic information

Entry
Database: PDB / ID: 4iby
TitleHuman p53 core domain with hot spot mutation R273H and second-site suppressor mutation S240R
ComponentsCellular tumor antigen p53
KeywordsDNA BINDING PROTEIN / METAL-BINDING / LOOP-SHEET-HELIX MOTIF / TRANSCRIPTION / ACTIVATOR / ANTI-ONCOGENE / APOPTOSIS / CELL CYCLE / DISEASE MUTATION / RESCUE MUTATION / TUMOR SUPPRESSOR
Function / homology
Function and homology information


Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / 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 ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / negative regulation of helicase activity / 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 / regulation of fibroblast apoptotic process / intrinsic apoptotic signaling pathway in response to hypoxia / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / oxidative stress-induced premature senescence / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / germ cell nucleus / RUNX3 regulates CDKN1A transcription / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / 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 / T cell lineage commitment / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of mitophagy / cardiac septum morphogenesis / negative regulation of DNA replication / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / negative regulation of telomere maintenance via telomerase / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / necroptotic process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / 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 / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / positive regulation of execution phase of apoptosis / Transcriptional Regulation by VENTX / replicative senescence / cellular response to UV-C / general transcription initiation factor binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to actinomycin D / neuroblast proliferation / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / type II interferon-mediated signaling pathway / hematopoietic stem cell differentiation / Pyroptosis / chromosome organization / viral process / embryonic organ development / somitogenesis / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / glial cell proliferation / hematopoietic progenitor cell differentiation / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / cellular response to glucose starvation / cis-regulatory region sequence-specific DNA binding / mitophagy / negative regulation of fibroblast proliferation / positive regulation of cardiac muscle cell apoptotic process / positive regulation of intrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / negative regulation of proteolysis / Regulation of TP53 Activity through Acetylation / mitotic G1 DNA damage checkpoint signaling / gastrulation / 14-3-3 protein binding / response to salt stress / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription repressor complex
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
Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsEldar, A. / Rozenberg, H. / Diskin-Posner, Y. / Shakked, Z.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural studies of p53 inactivation by DNA-contact mutations and its rescue by suppressor mutations via alternative protein-DNA interactions.
Authors: Eldar, A. / Rozenberg, H. / Diskin-Posner, Y. / Rohs, R. / Shakked, Z.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,67911
Polymers45,1132
Non-polymers5659
Water13,565753
1
A: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7464
Polymers22,5571
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9327
Polymers22,5571
Non-polymers3766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.524, 69.212, 67.195
Angle α, β, γ (deg.)90.000, 96.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 22556.650 Da / Num. of mol.: 2 / Fragment: DNA binding domain / Mutation: R273H, S240R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P53, TP53 / Plasmid: pET-27-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04637
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 20% PEG 3350, 0.2M Na2HPO4, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 27, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. obs: 69956 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.145 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.474.10.53734721.0061100
1.47-1.540.55635421.042199.9
1.5-1.534.10.45434731.061100
1.53-1.5640.37934741.078199.8
1.56-1.64.10.34834841.1251100
1.6-1.634.10.30434961.136199.8
1.63-1.674.10.24834991.138199.8
1.67-1.724.10.22134881.1661100
1.72-1.774.10.18934901.217199.5
1.77-1.834.10.1634771.258199.5
1.83-1.894.10.14234991.27199.3
1.89-1.974.20.10934711.382199.7
1.97-2.064.20.08934991.259199.6
2.06-2.174.20.07534991.215199.6
2.17-2.34.20.07434781.393199.7
2.3-2.484.30.0635311.134199.9
2.48-2.734.40.05235161.061199.9
2.73-3.124.40.04335340.979199.9
3.12-3.934.20.03834560.985197.9
3.93-254.20.03835781.01199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TSR

1tsr


Resolution: 1.45→21.779 Å / Occupancy max: 1 / Occupancy min: 0.02 / FOM work R set: 0.8772 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.89 / σ(I): 0 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 3524 5.05 %RANDOM
Rwork0.1694 ---
obs0.171 69847 99.49 %-
all-69847 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.39 Å2 / Biso mean: 14.5475 Å2 / Biso min: 3.43 Å2
Refinement stepCycle: LAST / Resolution: 1.45→21.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 30 753 3860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073434
X-RAY DIFFRACTIONf_angle_d1.134689
X-RAY DIFFRACTIONf_chiral_restr0.076511
X-RAY DIFFRACTIONf_plane_restr0.005628
X-RAY DIFFRACTIONf_dihedral_angle_d12.8731340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46940.2651440.23672598274299
1.4694-1.49040.25921340.228726802814100
1.4904-1.51260.23771270.216226752802100
1.5126-1.53630.23431290.199226492778100
1.5363-1.56140.23871520.198526282780100
1.5614-1.58840.22411640.186626442808100
1.5884-1.61720.2091370.185526562793100
1.6172-1.64830.21621330.180626612794100
1.6483-1.6820.21551390.177226842823100
1.682-1.71850.21861410.171226222763100
1.7185-1.75850.21141590.17322621278099
1.7585-1.80240.21861400.169926512791100
1.8024-1.85110.19941420.17482638278099
1.8511-1.90560.20011250.18912632275799
1.9056-1.9670.29831410.19992653279499
1.967-2.03730.21591390.164526642803100
2.0373-2.11880.19831450.16452610275599
2.1188-2.21510.22821480.17442666281499
2.2151-2.33180.21271420.17862640278299
2.3318-2.47770.19351360.162726792815100
2.4777-2.66870.20511300.163626532783100
2.6687-2.93670.19551520.167326962848100
2.9367-3.36030.18371450.158226792824100
3.3603-4.22850.14361350.13322621275697
4.2285-21.78160.15211450.14982723286899
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)
12.09860.2556-0.8041.4621-0.32392.85380.0606-0.0868-0.11380.0773-0.0664-0.08430.16590.31230.00060.10660.0024-0.03680.12470.04150.10919.555-0.947340.1622
20.43230.11580.00961.28430.25540.54470.0101-0.0491-0.10650.026-0.02280.01350.0213-0.03290.00860.0835-0.0064-0.01120.06570.02180.0744-4.4268-7.08533.2144
31.08690.4783-0.77510.33470.06712.309-0.0432-0.0113-0.07510.0001-0.0016-0.062-0.0050.15440.03640.07570.00490.01260.04090.01290.06697.7254.74126.3311
40.85510.5035-1.11922.60670.84126.7441-0.01620.21710.23620.0109-0.11280.286-0.4751-0.70970.10830.14470.0275-0.00350.1340.02370.142-5.942812.464622.1948
50.85410.2818-0.50951.86631.46617.53180.07140.03640.01710.0337-0.19650.2369-0.0891-0.64380.12220.0618-0.00820.01030.09320.00990.0733-9.49437.805336.9279
62.3676-0.4507-1.96191.3408-0.15591.86640.1129-0.18540.3797-0.04780.0309-0.1343-0.20330.1799-0.12220.0817-0.01790.00490.0658-0.01210.09045.719115.628832.639
70.8795-0.44550.25851.94910.84010.61720.1136-0.0961-0.09150.4090.17260.51530.2023-0.4739-0.18990.1374-0.0528-0.00570.14050.06880.1269-5.99170.80843.896
81.90560.61910.36361.8051-1.07410.9556-0.04120.2504-0.0849-0.18740.0192-0.08390.1083-0.05080.05010.0751-0.00620.00350.043-0.00470.0668-1.19270.739922.4812
90.65790.03310.70630.80290.28182.52470.0293-0.0016-0.00480.03720.0016-0.05190.0550.0857-0.03290.0807-0.00570.0040.06740.02260.08173.2588-0.332834.2529
106.31171.90022.79873.9785-1.86436.41930.09550.6548-0.4267-0.62460.065-0.3090.39690.436-0.09150.22970.00490.01620.107-0.0370.1127-0.9342-16.508120.5777
110.9275-0.20910.13761.1892-0.16090.4667-0.0176-0.0142-0.036-0.0230.0185-0.0272-0.03630.0234-0.00110.0541-0.0128-0.00220.0456-0.00340.060924.29823.71652.7891
121.6041-0.2505-0.92160.6918-0.20631.63660.0275-0.02620.01520.1140.04240.0173-0.0553-0.1029-0.06030.0637-0.00880.00960.0356-0.00140.059117.938213.125312.9006
136.031-0.675-2.17032.45740.44242.69760.04770.5398-0.451-0.1771-0.08550.38580.3893-0.7820.04440.1472-0.0491-0.03370.1806-0.01070.18511.01425.05040.6506
142.25620.0047-0.79232.0850.16972.1695-0.02630.0882-0.0727-0.0422-0.02310.00570.16650.01020.03080.0317-0.0016-0.00920.022-0.01270.047723.25236.26522.7103
152.01841.2898-0.3553.5891-1.10011.3636-0.01840.29360.0487-0.3909-0.0165-0.2861-0.1463-0.00150.03610.11260.0040.03050.07220.01170.076331.452317.4747-4.6171
161.07351.05120.13081.5261-0.64481.18520.07440.06690.040.10580.03950.1948-0.0576-0.3612-0.12150.0630.0132-0.00120.09260.01110.086711.832116.72475.0629
173.8506-0.95710.03711.24070.19920.7352-0.0236-0.1126-0.00560.05080.057-0.03070.02520.0057-0.03750.0443-0.009-0.00760.04410.00580.049426.85817.1847.6233
185.1237-0.22760.46546.3196-0.02484.87920.0394-0.35990.2730.3-0.0450.3303-0.1891-0.30290.05870.06940.01750.02370.07180.00340.10969.317933.07285.3646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 94:112 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 113:155 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 156:176 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 177:194 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 195:203 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 204:213 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 214:229 )A0
8X-RAY DIFFRACTION8CHAIN A AND (RESID 230:250 )A0
9X-RAY DIFFRACTION9CHAIN A AND (RESID 251:277 )A0
10X-RAY DIFFRACTION10CHAIN A AND (RESID 278:289 )A0
11X-RAY DIFFRACTION11CHAIN B AND (RESID 94:155 )B0
12X-RAY DIFFRACTION12CHAIN B AND (RESID 156:176 )B0
13X-RAY DIFFRACTION13CHAIN B AND (RESID 177:194 )B0
14X-RAY DIFFRACTION14CHAIN B AND (RESID 195:213 )B0
15X-RAY DIFFRACTION15CHAIN B AND (RESID 214:229 )B0
16X-RAY DIFFRACTION16CHAIN B AND (RESID 230:250 )B0
17X-RAY DIFFRACTION17CHAIN B AND (RESID 251:274 )B0
18X-RAY DIFFRACTION18CHAIN B AND (RESID 275:289 )B0

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