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- PDB-7nmz: Structure of 14-3-3 eta in complex with Nedd4-2(335-455) containi... -

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Basic information

Entry
Database: PDB / ID: 7nmz
TitleStructure of 14-3-3 eta in complex with Nedd4-2(335-455) containing two 14-3-3 binding motifs Ser342 and Ser448
Components
  • 14-3-3 protein eta
  • E3 ubiquitin-protein ligase NEDD4-like
KeywordsSIGNALING PROTEIN / E3 ubiquitin protein ligase / complex / Nedd4-2 / 14-3-3 protein
Function / homology
Function and homology information


glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / negative regulation of dendrite morphogenesis / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / intracellular glucocorticoid receptor signaling pathway ...glucocorticoid catabolic process / cerebellar granule cell to Purkinje cell synapse / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / negative regulation of dendrite morphogenesis / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / intracellular glucocorticoid receptor signaling pathway / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / nuclear glucocorticoid receptor binding / positive regulation of dendrite extension / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / HECT-type E3 ubiquitin transferase / membrane depolarization during action potential / sodium channel inhibitor activity / regulation of monoatomic ion transmembrane transport / regulation of neuron differentiation / regulation of dendrite morphogenesis / regulation of membrane depolarization / protein monoubiquitination / intercalated disc / sodium channel regulator activity / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / protein K48-linked ubiquitination / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / regulation of sodium ion transport / RHO GTPases activate PKNs / monoatomic ion transmembrane transport / insulin-like growth factor receptor binding / substantia nigra development / presynaptic modulation of chemical synaptic transmission / multivesicular body / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Downregulation of SMAD2/3:SMAD4 transcriptional activity / intracellular protein transport / regulation of synaptic plasticity / Budding and maturation of HIV virion / regulation of protein stability / Stimuli-sensing channels / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / actin binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein ubiquitination / protein heterodimerization activity / protein domain specific binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / signal transduction / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 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 / C2 domain superfamily
Similarity search - Domain/homology
14-3-3 protein eta / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsPohl, P. / Obsil, T. / Obsilova, V.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation20-00058S Czech Republic
CitationJournal: Commun Biol / Year: 2021
Title: 14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains.
Authors: Pohl, P. / Joshi, R. / Petrvalska, O. / Obsil, T. / Obsilova, V.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
AA: 14-3-3 protein eta
BA: 14-3-3 protein eta
C: E3 ubiquitin-protein ligase NEDD4-like


Theoretical massNumber of molelcules
Total (without water)67,8163
Polymers67,8163
Non-polymers00
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-27 kcal/mol
Surface area23010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.860, 58.950, 106.760
Angle α, β, γ (deg.)90.000, 90.693, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein 14-3-3 protein eta / Protein AS1


Mass: 27186.777 Da / Num. of mol.: 2 / Mutation: S235Stop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAH, YWHA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04917
#2: Protein E3 ubiquitin-protein ligase NEDD4-like / HECT-type E3 ubiquitin transferase NED4L / NEDD4.2 / Nedd4-2


Mass: 13442.557 Da / Num. of mol.: 1 / Mutation: T367A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96PU5, HECT-type E3 ubiquitin transferase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M of each NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1Mbicine/Trizma base pH 8.5, 30% sacharose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2.303→32.69 Å / Num. obs: 32703 / % possible obs: 99.86 % / Redundancy: 4.73 % / Biso Wilson estimate: 33.19 Å2 / Rrim(I) all: 0.064 / Net I/σ(I): 19.68
Reflection shellResolution: 2.303→2.385 Å / Redundancy: 3.99 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 3215 / Rrim(I) all: 0.655

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C63

2c63


Resolution: 2.303→32.69 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5299
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1641 5.02 %Random selection
Rwork0.1993 31049 --
obs0.2012 32690 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.92 Å2
Refinement stepCycle: LAST / Resolution: 2.303→32.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3718 0 0 189 3907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343768
X-RAY DIFFRACTIONf_angle_d0.60995097
X-RAY DIFFRACTIONf_chiral_restr0.0348586
X-RAY DIFFRACTIONf_plane_restr0.0036658
X-RAY DIFFRACTIONf_dihedral_angle_d3.7952531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.30151340.24622552X-RAY DIFFRACTION99.3
2.37-2.450.26331380.22422588X-RAY DIFFRACTION99.96
2.45-2.530.28851250.22612563X-RAY DIFFRACTION99.96
2.53-2.640.25231330.2132571X-RAY DIFFRACTION100
2.64-2.760.26081360.21072562X-RAY DIFFRACTION100
2.76-2.90.29361390.21542579X-RAY DIFFRACTION100
2.9-3.080.25871340.21872577X-RAY DIFFRACTION100
3.08-3.320.26921400.21152597X-RAY DIFFRACTION100
3.32-3.650.22411400.19942592X-RAY DIFFRACTION99.96
3.65-4.180.20641370.17452594X-RAY DIFFRACTION100
4.18-5.270.20041400.17662598X-RAY DIFFRACTION100
5.27-32.690.20341450.19292676X-RAY DIFFRACTION99.58

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