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- PDB-3p1s: Crystal structure of human 14-3-3 sigma C38N/N166H in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3p1s
TitleCrystal structure of human 14-3-3 sigma C38N/N166H in complex with TASK-3 peptide and stabilizer fusicoccin A
Components
  • 14-3-3 protein sigma
  • 6-mer peptide from Potassium channel subfamily K member 9
KeywordsPEPTIDE BINDING PROTEIN / Helical protein / Phosphoprotein / Adapter protein / Nucleus
Function / homology
Function and homology information


TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity / potassium ion import across plasma membrane / positive regulation of epidermal cell differentiation / keratinocyte development ...TWIK-releated acid-sensitive K+ channel (TASK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / regulation of epidermal cell division / protein kinase C inhibitor activity / potassium ion import across plasma membrane / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / potassium channel activity / 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 / potassium ion transmembrane transport / 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 / potassium ion transport / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle / 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 / 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
FUSICOCCIN / 14-3-3 protein sigma / Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAnders, C. / Higuchi, Y. / Schumacher, B. / Thiel, P. / Kato, N. / 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
DepositionSep 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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

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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: 6-mer peptide from Potassium channel subfamily K member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1856
Polymers27,4202
Non-polymers7654
Water4,504250
1
A: 14-3-3 protein sigma
P: 6-mer peptide from Potassium channel subfamily K member 9
hetero molecules

A: 14-3-3 protein sigma
P: 6-mer peptide from Potassium channel subfamily K member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,37012
Polymers54,8404
Non-polymers1,5308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4010 Å2
ΔGint-11 kcal/mol
Surface area23420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.210, 111.180, 62.350
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-252-

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: 26562.947 Da / Num. of mol.: 1 / Mutation: C38V, N166H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN / Plasmid: pPROEX HTB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P31947
#2: Protein/peptide 6-mer peptide from Potassium channel subfamily K member 9 / TASK-3 peptide


Mass: 856.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: Q9NPC2

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Non-polymers , 4 types, 254 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.095M HEPES Na-Salt, 25.6% PEG 400, 0.19M CaCl2, 5% Glycerol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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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: Jun 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→19.83 Å / Num. all: 34745 / Num. obs: 34326 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.54 % / Biso Wilson estimate: 20.899 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 32.8
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 9.81 / Num. unique all: 2830 / % possible all: 96.9

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Processing

Software
NameVersionClassification
MAR345softwaredata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LW1

3lw1


Resolution: 1.65→19.83 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.02 / SU ML: 0.048 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20096 1717 5 %RANDOM
Rwork0.14519 ---
obs0.14797 32608 100 %-
all-34326 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.684 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 51 250 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222296
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0362.0233177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.665326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.424.537108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32215.032465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0781518
X-RAY DIFFRACTIONr_chiral_restr0.1460.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021743
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.21.51357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.29622234
X-RAY DIFFRACTIONr_scbond_it5.1093939
X-RAY DIFFRACTIONr_scangle_it7.2344.5891
X-RAY DIFFRACTIONr_rigid_bond_restr2.66832296
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 123 -
Rwork0.188 2332 -
obs-2332 100 %

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