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- PDB-3lw1: Binary complex of 14-3-3 sigma and p53 pT387-peptide -

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Basic information

Entry
Database: PDB / ID: 3lw1
TitleBinary complex of 14-3-3 sigma and p53 pT387-peptide
Components
  • 14-3-3 protein sigma
  • peptide of Cellular tumor antigen p53
KeywordsPEPTIDE BINDING PROTEIN / adapter protein / Cytoplasm / Nucleus / Phosphoprotein
Function / homology
Function and homology information


negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of fibroblast apoptotic process / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 helicase activity / signal transduction by p53 class mediator / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of fibroblast apoptotic process / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / : / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / germ cell nucleus / regulation of tissue remodeling / ATP-dependent DNA/DNA annealing activity / thymocyte apoptotic process / oligodendrocyte apoptotic process / oxidative stress-induced premature senescence / positive regulation of mitochondrial membrane permeability / positive regulation of thymocyte apoptotic process / bone marrow development / cellular response to actinomycin D / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / circadian behavior / T cell lineage commitment / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / B cell lineage commitment / 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 / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of TP53 Activity through Association with Co-factors / ER overload response / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / neuroblast proliferation / positive regulation of epidermal cell differentiation / cardiac septum morphogenesis / keratinocyte development / necroptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / regulation of epidermal cell division / protein kinase C inhibitor activity / keratinization / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / hematopoietic stem cell differentiation / keratinocyte proliferation / negative regulation of mitophagy / Zygotic genome activation (ZGA) / somitogenesis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / regulation of cell-cell adhesion / Association of TriC/CCT with target proteins during biosynthesis / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / rRNA transcription / negative regulation of reactive oxygen species metabolic process / replicative senescence / establishment of skin barrier / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / TFIID-class transcription factor complex binding / Transcriptional Regulation by VENTX / cellular response to UV-C / hematopoietic progenitor cell differentiation / Regulation of localization of FOXO transcription factors / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of keratinocyte proliferation / embryonic organ development / chromosome organization / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / general transcription initiation factor binding / response to X-ray / positive regulation of execution phase of apoptosis / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / type II interferon-mediated signaling pathway / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / negative regulation of protein localization to plasma membrane / cAMP/PKA signal transduction / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / glial cell proliferation / cellular response to glucose starvation
Similarity search - Function
Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / 14-3-3 domain / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain ...Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / 14-3-3 domain / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / Delta-Endotoxin; domain 1 / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / p53-like transcription factor, DNA-binding / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cellular tumor antigen p53 / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsSchumacher, B. / Mondry, J. / Thiel, P. / Weyand, M. / Ottmann, C.
CitationJournal: Febs Lett. / Year: 2010
Title: Structure of the p53 C-terminus bound to 14-3-3: Implications for stabilization of the p53 tetramer
Authors: Schumacher, B. / Mondry, J. / Thiel, P. / Weyand, M. / Ottmann, C.
History
DepositionFeb 23, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: peptide of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5037
Polymers29,3032
Non-polymers2005
Water7,278404
1
A: 14-3-3 protein sigma
P: peptide of Cellular tumor antigen p53
hetero molecules

A: 14-3-3 protein sigma
P: peptide of Cellular tumor antigen p53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00614
Polymers58,6054
Non-polymers40110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4350 Å2
ΔGint-20 kcal/mol
Surface area23810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.320, 112.320, 62.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-251-

MG

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein 14-3-3 protein sigma / Stratifin / Epithelial cell marker protein 1


Mass: 28226.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, SFN / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P31947
#2: Protein/peptide peptide of Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 1075.986 Da / Num. of mol.: 1 / Fragment: UNP residues 385-393 / Source method: obtained synthetically
Details: synthetic peptide, the full length protein p53 occurs in homo sapiens
References: UniProt: P04637

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Non-polymers , 4 types, 409 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.2M calcium chloride, 28% PEG 400, 5% glycerol, 2mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.85 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: Si(111) monochromator (horizontal) and Dynamically bendable mirror (vertical)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.28→45.57 Å / Num. obs: 74319 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 18.258 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 20.8
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3304 / % possible all: 98.2

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YWT

1ywt


Resolution: 1.28→45.57 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.952 / SU ML: 0.019 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.151 3716 5 %RANDOM
Rwork0.126 ---
all0.128 74319 --
obs0.128 70603 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.131 Å / Luzzati d res low obs: 45.57 Å
Refinement stepCycle: LAST / Resolution: 1.28→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 10 404 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222229
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9973066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8175.062322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60324.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.981516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021707
X-RAY DIFFRACTIONr_mcbond_it2.4331.51341
X-RAY DIFFRACTIONr_mcangle_it3.62122196
X-RAY DIFFRACTIONr_scbond_it5.2333888
X-RAY DIFFRACTIONr_scangle_it7.5934.5819
X-RAY DIFFRACTIONr_rigid_bond_restr2.81632229
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 268 -
Rwork0.136 5098 -
obs-5098 100 %

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