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- PDB-5nwi: 14-3-3c in complex with CPP -

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Basic information

Entry
Database: PDB / ID: 5nwi
Title14-3-3c in complex with CPP
Components
  • 14-3-3 c-1 protein
  • Potassium channel KAT1
KeywordsSIGNALING PROTEIN / 14-3-3 / complex / fusicoccin / channel
Function / homology
Function and homology information


inward rectifier potassium channel activity / monoatomic ion channel complex / signal transduction / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / 14-3-3 domain / Delta-Endotoxin; domain 1 / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Potassium channel KAT/AKT / KHA domain / KHA, dimerisation domain of potassium ion channel / KHA domain profile. / Potassium channel, voltage-dependent, EAG/ELK/ERG / 14-3-3 domain / Delta-Endotoxin; domain 1 / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / 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 / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / 14-3-3-like protein C / Potassium channel KAT1 / 14-3-3 c-1 protein
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSaponaro, A. / Porro, A. / Chaves-Sanjuan, A. / Nardini, M. / Thiel, G. / Moroni, A.
CitationJournal: Plant Cell / Year: 2017
Title: Fusicoccin Activates KAT1 Channels by Stabilizing Their Interaction with 14-3-3 Proteins.
Authors: Saponaro, A. / Porro, A. / Chaves-Sanjuan, A. / Nardini, M. / Rauh, O. / Thiel, G. / Moroni, A.
History
DepositionMay 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 c-1 protein
P: Potassium channel KAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3103
Polymers30,2512
Non-polymers591
Water2,684149
1
A: 14-3-3 c-1 protein
P: Potassium channel KAT1
hetero molecules

A: 14-3-3 c-1 protein
P: Potassium channel KAT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6206
Polymers60,5014
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area4690 Å2
ΔGint-26 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.177, 110.177, 136.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-535-

HOH

31A-538-

HOH

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Components

#1: Protein 14-3-3 c-1 protein / 14-3-3 protein / 14-3-3-like protein C


Mass: 29554.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Initial PG do not belongs to the natural protein sequence
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: 14-3-3 c-1, LOC107777576, Nt14-3-3omega2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5KTN5, UniProt: P93343*PLUS
#2: Protein/peptide Potassium channel KAT1


Mass: 696.600 Da / Num. of mol.: 1 / Fragment: UNP residues 673-677 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q39128
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 400, 0.2 M ammonium acetate pH 7.0, 0.1 M sodium citrate pH 4.4, 10mM DTT and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.35→47.71 Å / Num. obs: 21014 / % possible obs: 100 % / Observed criterion σ(I): 5.1 / Redundancy: 39 % / Biso Wilson estimate: 32.28 Å2 / CC1/2: 0.971 / Rpim(I) all: 0.045 / Net I/σ(I): 15.2
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 27.7 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 2044 / CC1/2: 0.706 / Rpim(I) all: 0.365 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O9D
Resolution: 2.35→45.043 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1093 5.2 %
Rwork0.1957 --
obs0.1983 21012 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→45.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 4 149 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132002
X-RAY DIFFRACTIONf_angle_d1.1512702
X-RAY DIFFRACTIONf_dihedral_angle_d31.222762
X-RAY DIFFRACTIONf_chiral_restr0.061299
X-RAY DIFFRACTIONf_plane_restr0.007352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4570.35471190.33692442X-RAY DIFFRACTION100
2.457-2.58650.36471330.31212425X-RAY DIFFRACTION100
2.5865-2.74850.30491530.27162431X-RAY DIFFRACTION100
2.7485-2.96070.30631420.24442439X-RAY DIFFRACTION100
2.9607-3.25860.32091370.22092472X-RAY DIFFRACTION100
3.2586-3.72990.23411160.17622508X-RAY DIFFRACTION100
3.7299-4.69850.1651280.12812530X-RAY DIFFRACTION100
4.6985-45.05160.19061650.14842672X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.3471.60210.84185.66310.48053.65990.1629-0.60860.33090.5643-0.25870.46970.2537-0.40780.1080.35890.05410.08680.52280.04990.325-45.312538.872123.6239
23.01571.8331.53542.86991.61413.5838-0.10170.01620.2215-0.2181-0.05450.1276-0.0426-0.17120.20660.260.0940.01390.18420.0690.2804-40.406936.56957.0292
32.29251.33650.82024.14680.73932.2018-0.163-0.04210.2358-0.47410.01340.3912-0.1064-0.46170.130.34650.11160.00180.34150.08640.29-43.180341.30012.1284
44.7643-1.00860.45361.7851-1.10454.010.03480.40690.2771-0.32110.00080.0886-0.56680.0049-0.01320.33280.06540.02390.17280.06220.2704-29.083747.89121.3232
52.12613.58981.94526.92024.17622.53190.1313-0.00060.12110.00230.0171-0.3195-0.49540.0076-0.6630.4584-0.02480.08630.6339-0.07420.3274-15.2244.40085.3173
64.1173-0.7129-1.86953.74221.0390.9987-0.00940.5258-0.79970.16060.112-0.09751.01790.6712-0.08230.63020.187-0.05320.46230.00040.5433-19.102734.91232.0965
72.19341.7350.9329.3377-1.2870.90880.59970.263-0.9218-0.90340.5348-1.25070.1952-0.0433-1.40670.4621-0.0481-0.02090.4297-0.1070.5043-30.042334.94761.7832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 193 )
5X-RAY DIFFRACTION5chain 'A' and (resid 194 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 243 )
7X-RAY DIFFRACTION7chain 'P' and (resid 673 through 677 )

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