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- PDB-6ghp: 14-3-3sigma in complex with a TASK3 peptide stabilized by semi-sy... -

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Basic information

Entry
Database: PDB / ID: 6ghp
Title14-3-3sigma in complex with a TASK3 peptide stabilized by semi-synthetic natural product FC-NAc
Components
  • 14-3-3 protein sigma
  • Potassium channel subfamily K member 9
KeywordsSIGNALING PROTEIN / Potassium channel / natural product / PPI / stabilizer
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
Chem-EZ5 / 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: 1.95 Å
AuthorsAndrei, S.A. / de Vink, P.J. / Brunsveld, L. / Ottmann, C. / Higuchi, Y.
Funding support Netherlands, Japan, 4items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchECHO -STIP 717.014.001 Netherlands
Netherlands Organisation for Scientific ResearchGravity program 024.001.035 Netherlands
Japan Society for the Promotion of ScienceKAKENHI Grant JP 16K21138 Japan
Japan Agency for Medical Research and Development (AMED)Platform Project for Supporting Drug Discovery and Life Science Research Japan
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Rationally Designed Semisynthetic Natural Product Analogues for Stabilization of 14-3-3 Protein-Protein Interactions.
Authors: Andrei, S.A. / de Vink, P. / Sijbesma, E. / Han, L. / Brunsveld, L. / Kato, N. / Ottmann, C. / Higuchi, Y.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Potassium channel subfamily K member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1616
Polymers27,4422
Non-polymers7194
Water4,396244
1
A: 14-3-3 protein sigma
P: Potassium channel subfamily K member 9
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)56,32212
Polymers54,8844
Non-polymers1,4388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4830 Å2
ΔGint-68 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.453, 111.473, 63.675
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-407-

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: 26558.914 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 Potassium channel subfamily K member 9 / Acid-sensitive potassium channel protein TASK-3 / TWIK-related acid-sensitive K(+) channel 3 / Two ...Acid-sensitive potassium channel protein TASK-3 / TWIK-related acid-sensitive K(+) channel 3 / Two pore potassium channel KT3.2 / Two pore K(+) channel KT3.2


Mass: 882.988 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Phosphorylated C-terminal 6-mer of potassium channel TASK3
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NPC2

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Non-polymers , 4 types, 248 molecules

#3: Chemical ChemComp-EZ5 / ~{N}-[(2~{S})-2-[(1~{E},3~{R},4~{S},8~{R},9~{R},10~{R},11~{S},14~{S})-14-(methoxymethyl)-3,10-dimethyl-8-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(2-methylbut-3-en-2-yloxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4,9-bis(oxidanyl)-6-tricyclo[9.3.0.0^{3,7}]tetradeca-1,6-dienyl]propyl]ethanamide


Mass: 637.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H55NO10 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.095 M HEPES, pH 7.1, 26% v/v PEG400, 0.19 M CaCl2, 5% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.95→45.92 Å / Num. obs: 21097 / % possible obs: 97 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.053 / Rrim(I) all: 0.14 / Net I/σ(I): 12.5 / Num. measured all: 141126 / Scaling rejects: 50
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-26.90.984939513640.7560.41.064289.6
8.94-45.924.80.02511932490.9990.0120.0284293.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.2 Å34.61 Å
Translation5.2 Å34.61 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→34.606 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2311 1037 4.92 %
Rwork0.1811 20049 -
obs0.1835 21086 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.44 Å2 / Biso mean: 34.2979 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.95→34.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 103 244 2165
Biso mean--47.04 41.26 -
Num. residues----229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.05280.33621700.25292609277990
2.0528-2.18140.25041200.20052763288394
2.1814-2.34980.21311300.17182868299898
2.3498-2.58620.22411500.17382887303798
2.5862-2.96030.24881490.17892909305899
2.9603-3.72890.20121450.16582964310999
3.7289-34.61180.22491730.18053049322299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.27340.65071.33562.9931-0.31873.01670.0336-0.0321-0.0381-0.2087-0.0030.152-0.0371-0.0348-0.0260.09280.0196-0.04340.11860.00060.1412-32.7212-12.4079-8.3797
20.9234-0.1536-0.10734.87272.56922.9204-0.001-0.0312-0.06880.30130.05480.12210.1773-0.0275-0.05460.10010.0352-0.01470.13820.03050.115-29.8908-9.42798.7619
32.90820.21811.73294.2987-1.21871.83370.0123-0.2736-0.52330.55460.14640.42160.234-0.0158-0.03450.22690.0410.0080.1630.0680.2044-26.9508-23.298813.0467
43.7742-2.657-0.5063.4619-1.30841.5615-0.0553-0.0033-0.225-0.043-0.07240.05260.20440.21090.15620.20410.0486-0.04490.21140.03050.2431-12.7539-25.570713.0652
51.6729-0.88381.2521.4693-1.78142.2612-0.2693-0.02580.18290.69010.00120.1684-0.4432-0.39580.31651.5950.49540.05010.7025-0.58440.2692-10.2017-28.3701-5.3906
64.61910.10611.11947.50223.90592.56170.35710.3922-0.21-0.10390.0659-0.8895-0.33440.6162-0.4620.16610.0235-0.0520.27150.00960.3256-7.6199-19.00858.9426
72.83753.87150.0967.23623.51916.0041-0.18550.28750.32290.0754-0.0628-0.3523-0.3436-0.02680.09860.18070.0464-0.08850.21570.01110.2667-15.709-12.645711.0987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 32 )A-4 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 113 )A33 - 113
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 161 )A114 - 161
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 207 )A162 - 207
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 212 )A208 - 212
6X-RAY DIFFRACTION6chain 'A' and (resid 213 through 231 )A213 - 231
7X-RAY DIFFRACTION7chain 'P' and (resid 370 through 374 )P370 - 374

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