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

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Basic information

Entry
Database: PDB / ID: 5mxo
TitleCrystal structure of 14-3-3sigma and a p53 C-terminal 12-mer synthetic phosphopeptide stabilized by Fusicoccin-A
Components
  • 14-3-3 protein sigma
  • p53 C-terminal 12 amino acids
KeywordsANTITUMOR PROTEIN / 14-3-3 p53 Fusicoccin antitumor protein
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 domain / Delta-Endotoxin; domain 1 / 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 domain / Delta-Endotoxin; domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FUSICOCCIN / 14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsAndrei, S. / Ottmann, C. / Leysen, S.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie CuriePIAP-GA-2011-286418 14-3-3stab Netherlands
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
DepositionJan 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 2.0Mar 13, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.occupancy / _pdbx_struct_assembly.details ..._atom_site.occupancy / _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 2.1Jan 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _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_type.id

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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: p53 C-terminal 12 amino acids
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7595
Polymers27,0182
Non-polymers7413
Water5,441302
1
A: 14-3-3 protein sigma
P: p53 C-terminal 12 amino acids
hetero molecules

A: 14-3-3 protein sigma
P: p53 C-terminal 12 amino acids
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,51810
Polymers54,0374
Non-polymers1,4816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6120 Å2
ΔGint-77 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.688, 111.560, 62.690
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-414-

HOH

21A-580-

HOH

31A-686-

HOH

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Components

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

#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) / References: UniProt: P31947
#2: Protein/peptide p53 C-terminal 12 amino acids


Mass: 475.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 305 molecules

#3: Chemical ChemComp-FSC / FUSICOCCIN / Fusicoccin


Mass: 680.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56O12
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.095 M HEPES, pH 7.1, 29% PEG 400, 0.19 M CaCl2, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.2→45.593 Å / Num. obs: 90414 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.061 / Net I/σ(I): 18.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.2-1.2210.81.4340.5150.4531.50699
6.57-45.59130.0480.9950.0140.0599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.18 Å45.59 Å
Translation6.18 Å45.59 Å

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Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lw1

3lw1


Resolution: 1.2→45.593 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.1
RfactorNum. reflection% reflection
Rfree0.1823 1738 1.92 %
Rwork0.1542 --
obs0.1547 90385 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.05 Å2 / Biso mean: 23.4886 Å2 / Biso min: 10 Å2
Refinement stepCycle: final / Resolution: 1.2→45.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 164 302 2251
Biso mean--34.13 34.53 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182198
X-RAY DIFFRACTIONf_angle_d1.6493005
X-RAY DIFFRACTIONf_chiral_restr0.098333
X-RAY DIFFRACTIONf_plane_restr0.011390
X-RAY DIFFRACTIONf_dihedral_angle_d22.139877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.23530.28671480.25587249739799
1.2353-1.27520.26711490.21673217470100
1.2752-1.32080.21461500.192373267476100
1.3208-1.37370.24471360.176573237459100
1.3737-1.43620.2031470.155573257472100
1.4362-1.51190.15751560.119673577513100
1.5119-1.60660.14421400.112773537493100
1.6066-1.73070.14741310.115473897520100
1.7307-1.90490.14931320.124374057537100
1.9049-2.18050.17551620.130674117573100
2.1805-2.74710.15731350.149274807615100
2.7471-45.62630.19711520.174877087860100

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