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- PDB-3sp5: Crystal structure of human 14-3-3 sigma C38V/N166H in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3sp5
TitleCrystal structure of human 14-3-3 sigma C38V/N166H in complex with TASK-3 peptide and stabilizer Cotylenol
Components
  • 14-3-3 protein sigma
  • TASK-3 peptide
KeywordsPEPTIDE BINDING PROTEIN / Helical protein / Phosphoprotein / Adapter protein
Function / homology
Function and homology information


negative regulation of aldosterone secretion / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity ...negative regulation of aldosterone secretion / regulation of action potential firing rate / TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / potassium ion leak channel activity / regulation of resting membrane potential / cellular response to acidic pH / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity / sodium channel activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / potassium ion import across plasma membrane / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / potassium channel activity / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / visual perception / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / potassium ion transport / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / synaptic vesicle / regulation of protein localization / positive regulation of cell growth / mitochondrial inner membrane / regulation of cell cycle / cadherin binding / protein heterodimerization activity / dendrite / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Potassium channel subfamily K member 9 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / 14-3-3 domain / Delta-Endotoxin; domain 1 / Potassium channel domain / Ion channel / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Potassium channel subfamily K member 9 / Two pore domain potassium channel, TASK family / Two pore domain potassium channel / 14-3-3 domain / Delta-Endotoxin; domain 1 / Potassium channel domain / Ion channel / 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
Cotylenol / 14-3-3 protein sigma / Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAnders, C. / Schumacher, B. / Ottmann, C.
CitationJournal: Chem.Biol. / Year: 2013
Title: A semisynthetic fusicoccane stabilizes a protein-protein interaction and enhances the expression of K+ channels at the cell surface.
Authors: Anders, C. / Higuchi, Y. / Koschinsky, K. / Bartel, M. / Schumacher, B. / Thiel, P. / Nitta, H. / Preisig-Muller, R. / Schlichthorl, G. / Renigunta, V. / Ohkanda, J. / Daut, J. / Kato, N. / Ottmann, C.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: TASK-3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7625
Polymers27,3632
Non-polymers3993
Water5,495305
1
A: 14-3-3 protein sigma
P: TASK-3 peptide
hetero molecules

A: 14-3-3 protein sigma
P: TASK-3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,52410
Polymers54,7264
Non-polymers7986
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4480 Å2
ΔGint-35 kcal/mol
Surface area23260 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-14 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.800, 111.560, 62.400
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-289-

HOH

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Components

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


Mass: 26505.896 Da / Num. of mol.: 1 / Mutation: C38V N166H
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 TASK-3 peptide


Mass: 856.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NPC2*PLUS
#3: Chemical ChemComp-CX7 / Cotylenol / (1R,3aS,4R,5R,6R,9aR,10E)-1-(methoxymethyl)-4,9a-dimethyl-7-(propan-2-yl)-1,2,3,3a,4,5,6,8,9,9a-decahydrodicyclopenta[a ,d][8]annulene-1,5,6-triol


Mass: 350.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.095M HEPES Na-Salt pH7.4, 25.6% PEG 400, 0.19M CaCl2, 5% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.5 Å / Num. all: 26853 / Num. obs: 26606 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.92 % / Biso Wilson estimate: 13.522 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.218.12151763883197.8
1.9-20.11311.51122973156198.7
2-2.250.0717.99224065711199
2.25-2.50.04625.13146293702199.7
2.5-30.03629.97168024221199.9
3-40.02641.12134023383199.9
4-60.02447.8268641775199.8
6-100.02349.262292616199.2
10-19.4890.02150.39508159182.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345softwaredata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3LW1

3lw1


Resolution: 1.8→19.49 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 2.06 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 1331 5 %RANDOM
Rwork0.1619 ---
obs0.1643 26606 100 %-
all-25275 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.13 Å2 / Biso mean: 13.522 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 27 305 2222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222154
X-RAY DIFFRACTIONr_angle_refined_deg2.04922961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8255300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88724.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93715.036419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0331517
X-RAY DIFFRACTIONr_chiral_restr0.1970.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021636
X-RAY DIFFRACTIONr_mcbond_it1.2051.51311
X-RAY DIFFRACTIONr_mcangle_it1.96522135
X-RAY DIFFRACTIONr_scbond_it3.3093843
X-RAY DIFFRACTIONr_scangle_it5.2654.5794
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 95 -
Rwork0.221 1794 -
all-1889 -
obs--100 %

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