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- PDB-5mhc: Crystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synt... -

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Basic information

Entry
Database: PDB / ID: 5mhc
TitleCrystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synthetic phosphopeptide
Components
  • 14-3-3 protein sigma
  • LYS-LEU-MET-PHE-LYS-TPO-GLU-GLY-PRO-ASP-SER-ASP
KeywordsANTITUMOR PROTEIN / 14-3-3 p53 C-terminus
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 / Activation of NOXA and translocation to mitochondria ...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 / Activation of NOXA and translocation to mitochondria / ATP-dependent DNA/DNA annealing activity / regulation of cell cycle G2/M phase transition / oligodendrocyte apoptotic process / negative regulation of miRNA processing / intrinsic apoptotic signaling pathway in response to hypoxia / oxidative stress-induced premature senescence / regulation of tissue remodeling / positive regulation of thymocyte apoptotic process / positive regulation of mitochondrial membrane permeability / germ cell nucleus / regulation of fibroblast apoptotic process / bone marrow development / cellular response to actinomycin D / circadian behavior / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / positive regulation of programmed necrotic cell death / : / RUNX3 regulates CDKN1A transcription / T cell proliferation involved in immune response / 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 / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / thymocyte apoptotic process / ER overload response / positive regulation of epidermal cell differentiation / keratinocyte development / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / regulation of epidermal cell division / necroptotic process / protein kinase C inhibitor activity / B cell lineage commitment / keratinization / entrainment of circadian clock by photoperiod / negative regulation of DNA replication / Zygotic genome activation (ZGA) / negative regulation of mitophagy / 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 / neuroblast proliferation / Association of TriC/CCT with target proteins during biosynthesis / 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 / keratinocyte proliferation / rRNA transcription / establishment of skin barrier / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway by p53 class mediator / TFIID-class transcription factor complex binding / Transcriptional Regulation by VENTX / Regulation of localization of FOXO transcription factors / cellular response to UV-C / replicative senescence / viral process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / hematopoietic stem cell differentiation / negative regulation of keratinocyte proliferation / embryonic organ development / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Pyroptosis / positive regulation of RNA polymerase II transcription preinitiation complex assembly / chromosome organization / general transcription initiation factor binding / positive regulation of execution phase of apoptosis / type II interferon-mediated signaling pathway / hematopoietic progenitor cell differentiation / cAMP/PKA signal transduction / negative regulation of stem cell proliferation / negative regulation of protein localization to plasma membrane / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to X-ray / somitogenesis / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of fibroblast proliferation / negative regulation of protein kinase activity / core promoter sequence-specific DNA binding
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 / molecular replacement / Resolution: 1.2 Å
AuthorsAndrei, S. / Ottmann, C. / Leysen, S.
Funding support1items
OrganizationGrant numberCountry
Marie Curie ActionPIAPP-GA-2011-286418 14-3-3Stabs
CitationJournal: FEBS Lett. / Year: 2017
Title: Small-molecule stabilization of the p53 - 14-3-3 protein-protein interaction.
Authors: Doveston, R.G. / Kuusk, A. / Andrei, S.A. / Leysen, S. / Cao, Q. / Castaldi, M.P. / Hendricks, A. / Brunsveld, L. / Chen, H. / Boyd, H. / Ottmann, C.
History
DepositionNov 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jan 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Oct 23, 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: LYS-LEU-MET-PHE-LYS-TPO-GLU-GLY-PRO-ASP-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0574
Polymers27,9922
Non-polymers642
Water6,125340
1
A: 14-3-3 protein sigma
P: LYS-LEU-MET-PHE-LYS-TPO-GLU-GLY-PRO-ASP-SER-ASP
hetero molecules

A: 14-3-3 protein sigma
P: LYS-LEU-MET-PHE-LYS-TPO-GLU-GLY-PRO-ASP-SER-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1148
Polymers55,9854
Non-polymers1294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area5190 Å2
ΔGint-32 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.114, 112.047, 62.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

CA

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Components

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


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P31947
#2: Protein/peptide LYS-LEU-MET-PHE-LYS-TPO-GLU-GLY-PRO-ASP-SER-ASP


Mass: 1449.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.095 M HEPES pH 7.5, 26% PEG400, 0.19 M CaCl2, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.2→45.44 Å / Num. obs: 90016 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 13.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.2-1.2211.31.0060.8681100
6.57-45.4412.80.0440.997199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
PHASER1.10.1_2155phasing
iMOSFLM7.2.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.2→45.44 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 17.94
RfactorNum. reflection% reflection
Rfree0.1652 1728 1.92 %
Rwork0.1503 --
obs0.1506 89954 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.47 Å2 / Biso mean: 20.4195 Å2 / Biso min: 6.9 Å2
Refinement stepCycle: final / Resolution: 1.2→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 2 340 2288
Biso mean--22.76 30.87 -
Num. residues----247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052255
X-RAY DIFFRACTIONf_angle_d0.8493083
X-RAY DIFFRACTIONf_chiral_restr0.058336
X-RAY DIFFRACTIONf_plane_restr0.005407
X-RAY DIFFRACTIONf_dihedral_angle_d14.634937
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2-1.23530.35961370.317672447381
1.2353-1.27520.28131650.26572637428
1.2752-1.32080.27241330.237372967429
1.3208-1.37370.19251470.182373107457
1.3737-1.43620.17241300.133573017431
1.4362-1.51190.13011550.114872987453
1.5119-1.60660.12071570.110873137470
1.6066-1.73070.15161350.120473587493
1.7307-1.90490.15211520.132273357487
1.9049-2.18050.1491230.131274067529
2.1805-2.74710.16331440.141474417585
2.7471-45.47740.16161500.161976617811

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