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- PDB-4fr3: Crystal structure of human 14-3-3 sigma in complex with TASK-3 pe... -

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Basic information

Entry
Database: PDB / ID: 4fr3
TitleCrystal structure of human 14-3-3 sigma in complex with TASK-3 peptide and stabilizer 16-O-Me-FC-H
Components
  • 14-3-3 protein sigma
  • TASK-3 peptide
KeywordsPEPTIDE BINDING PROTEIN/TOXIN / Nucleus / PEPTIDE BINDING PROTEIN-TOXIN complex
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 / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / sodium channel activity / regulation of cell-cell adhesion / potassium ion import across plasma membrane / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / Activation of BAD and translocation to mitochondria / phosphoserine residue binding / negative regulation of keratinocyte proliferation / establishment of skin barrier / potassium channel activity / 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 protein kinase activity / 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 / protein export from nucleus / negative regulation of innate immune response / 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 / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / potassium ion transport / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / regulation of cell cycle / mitochondrial inner membrane / 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 / cytoplasm / cytosol
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
Chem-0V4 / 14-3-3 protein sigma / Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOttmann, C. / Anders, C. / Schumacher, B.
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
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Sep 13, 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_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 1.3Dec 6, 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

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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)27,8475
Polymers27,3022
Non-polymers5453
Water2,360131
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)55,69410
Polymers54,6044
Non-polymers1,0906
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4260 Å2
ΔGint-26 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.680, 111.990, 62.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26444.812 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 TASK-3 peptide


Mass: 856.950 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NPC2*PLUS
#3: Sugar ChemComp-0V4 / (4R,5R,6R,6aS,9S,9aE,10aR)-5-hydroxy-9-(methoxymethyl)-6,10a-dimethyl-3-(propan-2-yl)-1,2,4,5,6,6a,7,8,9,10a-decahydrodicyclopenta[a,d][8]annulen-4-yl alpha-D-glucopyranoside / 16-O-Me-Fusicoccin H


Type: D-saccharide / Mass: 496.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C27H44O8
#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.: 131 / 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: 2.64 Å3/Da / Density % sol: 53.36 %
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
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 91462 / Rmerge(I) obs: 0.037 / D res high: 1.9 Å / Num. obs: 23065 / % possible obs: 99.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
101512696.210.019
81015697.510.021
6846199.610.024
46179799.710.024
34342599.910.026
2.53427499.910.038
2.22.5471499.910.057
2.12.2216999.710.084
22.1267099.910.115
1.92323999.810.171
ReflectionResolution: 1.9→19.6545 Å / Num. all: 23145 / Num. obs: 23065 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.037 / Net I/σ(I): 25.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-20.1718.22199.8
2-2.10.11511.57199.9
2.1-2.20.08415.54199.7
2.2-2.50.05721.34199.9
2.5-30.03829.61199.9
3-40.02643199.9
4-60.02449.98199.7
6-80.02449199.6
8-100.02153.59197.5
10-150.01953.8196.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345researchdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3lw1

3lw1


Resolution: 1.9→19.65 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.398 / SU ML: 0.073 / SU R Cruickshank DPI: 0.1306 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20863 1154 5 %RANDOM
Rwork0.16769 ---
obs0.16973 21911 100 %-
all-23065 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 37 131 1996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0582.0042808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.4925.072277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86324.16796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26415.039386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0451518
X-RAY DIFFRACTIONr_chiral_restr0.1560.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021540
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_it1.531.51252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35722018
X-RAY DIFFRACTIONr_scbond_it3.7643807
X-RAY DIFFRACTIONr_scangle_it6.0074.5764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 84 -
Rwork0.187 1587 -
obs--100 %

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