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- PDB-3ux0: Crystal structure of human 14-3-3 sigma in complex with TASK-3 pe... -

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Basic information

Entry
Database: PDB / ID: 3ux0
TitleCrystal structure of human 14-3-3 sigma in complex with TASK-3 peptide and stabilizer Fusicoccin H
Components
  • 14-3-3 protein sigma
  • TASK3 PHOSPHOPEPTIDE
KeywordsPEPTIDE BINDING PROTEIN / Helical protein / Phosphoprotein / Adapter protein / Nucleus
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-0DV / 14-3-3 protein sigma / Potassium channel subfamily K member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsThiel, P. / Bartel, M. / Anders, C. / Higuchi, Y. / Schumacher, B. / 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
DepositionDec 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: TASK3 PHOSPHOPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0669
Polymers27,3592
Non-polymers7077
Water5,999333
1
A: 14-3-3 protein sigma
P: TASK3 PHOSPHOPEPTIDE
hetero molecules

A: 14-3-3 protein sigma
P: TASK3 PHOSPHOPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,13218
Polymers54,7184
Non-polymers1,41514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4100 Å2
ΔGint-12 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.900, 111.040, 62.350
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-232-

MG

21A-252-

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: 26501.865 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 TASK3 PHOSPHOPEPTIDE


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

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Non-polymers , 5 types, 340 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-0DV / (4R,5R,6R,6aS,9S,9aE,10aR)-5-hydroxy-9-(hydroxymethyl)-6,10a-dimethyl-3-(propan-2-yl)-1,2,4,5,6,6a,7,8,9,10a-decahydrod icyclopenta[a,d][8]annulen-4-yl alpha-D-gulopyranoside / Fusicoccin H


Mass: 482.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H42O8
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.095M HEPES Na, 0.19M calcium chloride, 5% glycerol, 26.6% PEG400, pH 7.5, 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: Nov 11, 2011 / Details: mirrors
RadiationMonochromator: CURVED MULTILAYER MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→19.464 Å / Num. all: 28378 / Num. obs: 28378 / % possible obs: 97.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.86 % / Biso Wilson estimate: 24.991 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 23.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.75-1.850.2156.32149544390410493.5
1.85-20.1439.17189655055488096.5
2-2.40.08318.62423438159800798.1
2.4-2.70.0728.32264493342332099.3
2.7-30.05534.15171832158214699.4
3-40.03845.74268943376337399.9
4-60.03451.661388817701770100
6-80.03551.25345945545499.8
8-100.03257.111172163163100
10-120.03255.34897575100
120.03652.085331168674.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.46 Å
Translation2.5 Å19.46 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.46 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1467 / Occupancy max: 1 / Occupancy min: 0.08 / FOM work R set: 0.9016 / SU B: 1.813 / SU ML: 0.059 / SU R Cruickshank DPI: 0.1027 / SU Rfree: 0.1033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1419 5 %RANDOM
Rwork0.1515 ---
all0.1535 28378 --
obs0.1535 28378 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.36 Å2 / Biso mean: 19.6787 Å2 / Biso min: 2.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 45 333 2231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222201
X-RAY DIFFRACTIONr_angle_refined_deg1.7422.0093028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7425.065310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40824.954109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61715.034442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7151517
X-RAY DIFFRACTIONr_chiral_restr0.1210.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021673
X-RAY DIFFRACTIONr_mcbond_it1.0441.51305
X-RAY DIFFRACTIONr_mcangle_it1.82122137
X-RAY DIFFRACTIONr_scbond_it2.9313896
X-RAY DIFFRACTIONr_scangle_it4.7654.5850
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 97 -
Rwork0.189 1848 -
all-1945 -
obs--100 %

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