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- PDB-7ygi: Crystal structure of p53 DBD domain in complex with azurin -

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Basic information

Entry
Database: PDB / ID: 7ygi
TitleCrystal structure of p53 DBD domain in complex with azurin
Components
  • Azurin
  • Cellular tumor antigen p53
KeywordsANTITUMOR PROTEIN / Transient complex / tumour suppressor
Function / homology
Function and homology information


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 / Activation of NOXA and translocation to mitochondria / 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 / 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 / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / transition metal ion binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation
Similarity search - Function
Azurin / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / p53 family signature. ...Azurin / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / 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 / Cupredoxin
Similarity search - Domain/homology
: / PHOSPHATE ION / Azurin / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
Pseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJiang, W.X. / Zuo, J.Q. / Hu, J.J. / Chen, X.Q. / Ma, L.X. / Liu, Z. / Xing, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2021YFC2100100 China
CitationJournal: Commun Biol / Year: 2023
Title: Structural basis of bacterial effector protein azurin targeting tumor suppressor p53 and inhibiting its ubiquitination.
Authors: Hu, J. / Jiang, W. / Zuo, J. / Shi, D. / Chen, X. / Yang, X. / Zhang, W. / Ma, L. / Liu, Z. / Xing, Q.
History
DepositionJul 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release

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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: Azurin
D: Azurin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,67311
Polymers71,3234
Non-polymers3507
Water12,791710
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.839, 68.750, 83.847
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-360-

HOH

21D-386-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 93 through 105 or resid 107 through 289))
d_2ens_1(chain "B" and (resid 93 through 105 or resid 107...
d_1ens_2chain "C"
d_2ens_2(chain "D" and (resid 4 through 21 or (resid 22...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUGLYA1 - 13
d_12ens_1TYRLEUA15 - 197
d_21ens_1LEUGLYB2 - 14
d_22ens_1TYRLEUB16 - 198
d_11ens_2SERLEUC1 - 122
d_21ens_2SERLEUD2 - 123

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.987330982379, 0.026637123016, -0.156422488512), (-0.0206921887539, 0.999004819907, 0.0395120630686), (0.157319307649, -0.0357747603877, 0.986899590617)7.36841815141, 1.96168808609, -36.7206921172
2given(0.648750142655, 0.660224046272, 0.378454040973), (0.760474386834, -0.543941775006, -0.354691489005), (-0.0283188872442, 0.517910758845, -0.854965780893)-7.07332500395, 31.3620187024, -31.0499394503

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Cellular tumor antigen p53 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 22243.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli (E. coli) / References: UniProt: P04637
#2: Protein Azurin


Mass: 13418.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: azu, PA4922 / Production host: Escherichia coli (E. coli) / References: UniProt: P00282

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Non-polymers , 5 types, 717 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 298 K / Method: batch mode / Details: 0.05M Na2HPO4+19.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→19.88 Å / Num. obs: 46000 / % possible obs: 99.522 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.899 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 227437 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
PHENIXV 1.20.1-4487refinement
ADDREFdata reduction
ADDREFdata scaling
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KMD, 1E67

3kmd

1e67


Resolution: 2.1→19.876 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 2256 4.93 %
Rwork0.213 --
obs0.2158 45781 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 11 568 5547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095077
X-RAY DIFFRACTIONf_angle_d0.9666872
X-RAY DIFFRACTIONf_dihedral_angle_d3.4043082
X-RAY DIFFRACTIONf_chiral_restr0.056757
X-RAY DIFFRACTIONf_plane_restr0.007902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14560.33391510.27452772X-RAY DIFFRACTION99
2.1456-2.19550.4091310.32022763X-RAY DIFFRACTION98
2.1955-2.25030.47471290.41732241X-RAY DIFFRACTION81
2.2503-2.31110.48611250.39472444X-RAY DIFFRACTION87
2.3111-2.3790.3671310.27272797X-RAY DIFFRACTION99
2.379-2.45560.29231320.23952785X-RAY DIFFRACTION99
2.4556-2.54320.29651530.22542779X-RAY DIFFRACTION99
2.5432-2.64480.27411460.22642801X-RAY DIFFRACTION100
2.6448-2.76490.26281580.21222803X-RAY DIFFRACTION100
2.7649-2.91020.28691590.21252757X-RAY DIFFRACTION99
2.9102-3.09190.26151330.19382823X-RAY DIFFRACTION99
3.0919-3.32960.22111490.18652783X-RAY DIFFRACTION99
3.3296-3.66280.24521410.1882742X-RAY DIFFRACTION97
3.6628-4.18850.20841430.17092689X-RAY DIFFRACTION95
4.1885-5.26090.19521340.14822781X-RAY DIFFRACTION97
5.2609-100.21921410.1712765X-RAY DIFFRACTION95
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)
10.6646-0.284-0.08751.90080.1130.5882-0.00140.03610.0193-0.0594-0.0526-0.01320.02190.10530.04310.18680.00030.00240.13050.01670.0805-31.8582-25.4284-0.0822
20.8162-0.4178-0.41221.49660.64111.19440.0384-0.0033-0.0016-0.0423-0.03430.0123-0.0610.0004-0.00520.1939-0.00970.00670.1070.01560.0953-24.7391-22.7808-40.9365
31.4732-0.37140.21291.09-0.53280.9631-0.0993-0.0207-0.2966-0.06620.03170.43760.239-0.47610.03480.2085-0.0968-0.00650.3729-0.03880.3705-57.4904-20.4116-14.8108
41.38720.85470.11050.55510.09620.33950.07030.15180.112-0.18930.10580.7148-0.0733-0.4031-0.02790.176-0.0171-0.05180.51850.07860.6006-63.42464.0196-27.3107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 92 through 289)
2X-RAY DIFFRACTION2(chain 'B' and resid 92 through 289)
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 125)
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 125)

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