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- PDB-7nmi: Transactivation domain of p53 in complex with S100P, using annexi... -

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Basic information

Entry
Database: PDB / ID: 7nmi
TitleTransactivation domain of p53 in complex with S100P, using annexin A2 as crystallization chaperone
Components
  • Cellular tumor antigen p53
  • S100P-ANXA2 chimera
KeywordsPROTEIN BINDING / S100P / p53 / annexin A2 / protein-protein interaction / Ca2+-binding protein
Function / homology
Function and homology information


positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair ...positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / osteoclast development / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / 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 / Dissolution of Fibrin Clot / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / S100 protein binding / 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 / vesicle membrane / 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 / positive regulation of low-density lipoprotein receptor activity / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / epithelial cell apoptotic process / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / microvillus membrane / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / positive regulation of receptor recycling / ER overload response / negative regulation of DNA replication / 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 / phosphatidylserine binding / 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 / positive regulation of exocytosis / 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 / rRNA transcription / TFIID-class transcription factor complex binding / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / transition metal ion binding / mitophagy / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / regulation of neurogenesis
Similarity search - Function
S-100 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...S-100 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / 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 / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Cellular tumor antigen p53 / Annexin A2 / Protein S100-P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEcsedi, P. / Nyitray, L.
Funding support Hungary, 1items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH) Hungary
CitationJournal: To Be Published
Title: Transactivation domain of p53 in complex with S100P using annexin A2 as a crystallization chaperone
Authors: Ecsedi, P. / Nyitray, L.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: S100P-ANXA2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,49612
Polymers62,0432
Non-polymers45310
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Fluorescence polarization measurements were also carried out
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-129 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.920, 86.770, 113.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 4667.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637
#2: Protein S100P-ANXA2 chimera / Migration-inducing gene 9 protein / MIG9 / Protein S100-E / S100 calcium-binding protein P / ...Migration-inducing gene 9 protein / MIG9 / Protein S100-E / S100 calcium-binding protein P / Protein S100-P / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36 / Annexin A2


Mass: 57376.195 Da / Num. of mol.: 1 / Mutation: A238E
Source method: isolated from a genetically manipulated source
Details: A single chain S100P is fused to a annexin A2 molecule.
Source: (gene. exp.) Homo sapiens (human) / Gene: S100P, S100E, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25815, UniProt: P07355
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.86 % / Description: Needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Morpheus screen (MD) H6 0.1 M Amino acids, 0.1 M Buffer System 2, pH 7.5, 30 % v/v Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.636 Å / Num. obs: 38715 / % possible obs: 99.9 % / Redundancy: 11.636 % / Biso Wilson estimate: 46.417 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.132 / Χ2: 0.902 / Net I/σ(I): 22.47 / Num. measured all: 450497 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.159.3591.1653.0226401282728210.5281.24299.8
2.15-2.219.2740.9163.8725401274527390.6560.97899.8
2.21-2.289.2120.715.1124660268226770.7740.75999.8
2.28-2.359.0620.5956.2223680261526130.7910.63799.9
2.35-2.428.8840.4547.6822246251325040.8670.48799.6
2.42-2.518.950.4439.0121633242324170.8970.47399.8
2.51-2.613.1440.6811.5831098236623660.9450.707100
2.6-2.7114.0810.54614.2532190228622860.970.566100
2.71-2.8314.0340.42817.5530595218021800.9840.444100
2.83-2.9713.8620.32221.9729055209620960.9870.334100
2.97-3.1313.6340.23926.0127349200620060.9930.248100
3.13-3.3213.3640.17830.7225432190319030.9960.185100
3.32-3.5512.5080.12237.3522301178317830.9970.127100
3.55-3.8312.6320.08545.5221032166516650.9980.089100
3.83-4.213.8580.06354.7521535155415540.9990.066100
4.2-4.713.7720.05559.419391140814080.9960.058100
4.7-5.4213.370.05755.5316819125812580.9990.059100
5.42-6.6412.4170.05852.213336107410740.9990.061100
6.64-9.3912.1590.04361.47103968558550.9990.044100
9.39-47.63611.6610.03569.2659475175100.9990.03798.6

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata processing
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XJL

1xjl


Resolution: 2.1→47.636 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 2000 5.17 %
Rwork0.1941 36651 -
obs0.1958 38651 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.21 Å2 / Biso mean: 49.0082 Å2 / Biso min: 24.16 Å2
Refinement stepCycle: final / Resolution: 2.1→47.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 15 243 4374
Biso mean--46.08 48.42 -
Num. residues----520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.15260.33111390.2772566
2.1526-2.21080.24211420.24262575
2.2108-2.27580.25511410.22422593
2.2758-2.34930.2821410.22412581
2.3493-2.43320.28261400.23172565
2.4332-2.53060.24441420.21832607
2.5306-2.64580.27281410.21352574
2.6458-2.78530.24191420.20152597
2.7853-2.95980.25071420.19572618
2.9598-3.18830.22061420.19752614
3.1883-3.5090.23781440.19112635
3.509-4.01650.21381440.17612638
4.0165-5.05950.20131470.16662691
5.0595-47.6360.19831530.19142797
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)
11.00130.6509-0.13481.4836-0.17550.8475-0.11630.15790.0389-0.1820.1672-0.06040.06870.0615-0.05610.22490.0037-0.03020.27040.00240.238130.61266.1519-64.0433
22.75260.1102-3.80960.8317-0.70615.65160.40690.76220.7372-0.38590.1927-0.8254-0.73091.1052-0.50450.6674-0.25750.12831.1274-0.10740.890243.77556.6927-32.2251
39.9041-0.4445-1.32978.0033-4.2416.4354-0.0858-1.0318-0.20741.3245-0.05150.744-0.4578-0.6490.11280.6332-0.01480.01230.5909-0.07360.360923.4577-4.5547-16.9927
40.91810.37851.50213.92912.46815.1725-0.1199-0.10860.15230.28240.1429-0.35090.11080.2481-0.05560.29450.01990.0130.3087-0.00640.390333.8997-3.974-26.0846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 220 through 511 )B220 - 511
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 36 )A19 - 36
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 55 )A37 - 55
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 219 )B1 - 219

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