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- PDB-6zc9: Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding ... -

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Basic information

Entry
Database: PDB / ID: 6zc9
TitleStructure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448
Components
  • 14-3-3 protein gamma
  • E3 ubiquitin-protein ligase NEDD4-like
KeywordsSIGNALING PROTEIN / E3 ubiquitin protein ligase / complex / phosphorylation / 14-3-3 protein
Function / homology
Function and homology information


negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / : / positive regulation of cell-cell adhesion / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface ...negative regulation of sodium ion import across plasma membrane / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / : / positive regulation of cell-cell adhesion / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / phosphorylation-dependent protein binding / regulation of membrane repolarization / regulation of sodium ion transmembrane transport / regulation of membrane depolarization / potassium channel inhibitor activity / receptor catabolic process / positive regulation of dendrite extension / positive regulation of T cell mediated immune response to tumor cell / ventricular cardiac muscle cell action potential / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / regulation of neuron differentiation / regulation of dendrite morphogenesis / neuromuscular junction development / protein kinase C inhibitor activity / regulation of synapse organization / Regulation of localization of FOXO transcription factors / sodium channel regulator activity / protein monoubiquitination / Activation of BAD and translocation to mitochondria / regulation of signal transduction / potassium channel regulator activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein K48-linked ubiquitination / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / insulin-like growth factor receptor binding / multivesicular body / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Transcriptional and post-translational regulation of MITF-M expression and activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein sequestering activity / AURKA Activation by TPX2 / Downregulation of TGF-beta receptor signaling / protein kinase C binding / negative regulation of protein kinase activity / regulation of membrane potential / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Budding and maturation of HIV virion / regulation of protein stability / regulation of synaptic plasticity / receptor tyrosine kinase binding / receptor internalization / Stimuli-sensing channels / positive regulation of T cell activation / cellular response to insulin stimulus / positive regulation of protein catabolic process / neuron projection development / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / Antigen processing: Ubiquitination & Proteasome degradation / presynapse / regulation of protein localization / ubiquitin-dependent protein catabolic process / monoatomic ion transmembrane transport / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / mitochondrial matrix / apical plasma membrane / protein domain specific binding / focal adhesion / Golgi apparatus / signal transduction / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / 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 / 14-3-3 domain / Delta-Endotoxin; domain 1 / Protein kinase C conserved region 2 (CalB) ...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 / 14-3-3 domain / Delta-Endotoxin; domain 1 / Protein kinase C conserved region 2 (CalB) / C2 domain / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,1,1,3,3,3-hexafluoropropan-2-ol / 14-3-3 protein gamma / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89895988606 Å
AuthorsPohl, P. / Kalabova, D. / 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
DepositionJun 10, 2020Deposition 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 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
C: 14-3-3 protein gamma
D: 14-3-3 protein gamma
E: E3 ubiquitin-protein ligase NEDD4-like
F: E3 ubiquitin-protein ligase NEDD4-like
G: E3 ubiquitin-protein ligase NEDD4-like
H: E3 ubiquitin-protein ligase NEDD4-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,19012
Polymers112,5188
Non-polymers6724
Water9,836546
1
A: 14-3-3 protein gamma
C: 14-3-3 protein gamma
E: E3 ubiquitin-protein ligase NEDD4-like
G: E3 ubiquitin-protein ligase NEDD4-like


Theoretical massNumber of molelcules
Total (without water)56,2594
Polymers56,2594
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area23010 Å2
MethodPISA
2
B: 14-3-3 protein gamma
D: 14-3-3 protein gamma
F: E3 ubiquitin-protein ligase NEDD4-like
H: E3 ubiquitin-protein ligase NEDD4-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9318
Polymers56,2594
Non-polymers6724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-24 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.707, 205.707, 74.649
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
32
42
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROPROPRO(chain 'E' and (resid 444 or (resid 445 and (name...EE444 - 4501 - 7
221PROPROPROPROchain 'H'HH444 - 4501 - 7
132ASPASPGLNGLN(chain 'A' and (resid 3 through 5 or (resid 6...AA3 - 683 - 68
142LYSLYSTHRTHR(chain 'A' and (resid 3 through 5 or (resid 6...AA78 - 23478 - 234
252ASPASPGLNGLN(chain 'B' and (resid 3 through 5 or (resid 6...BB3 - 683 - 68
262LYSLYSTHRTHR(chain 'B' and (resid 3 through 5 or (resid 6...BB78 - 23478 - 234
372ASPASPGLNGLN(chain 'C' and (resid 3 through 5 or (resid 6...CC3 - 683 - 68
382LYSLYSTHRTHR(chain 'C' and (resid 3 through 5 or (resid 6...CC78 - 23478 - 234
492ASPASPGLNGLN(chain 'D' and (resid 3 through 67 or (resid 68...DD3 - 683 - 68
4102LYSLYSTHRTHR(chain 'D' and (resid 3 through 67 or (resid 68...DD78 - 23478 - 234
1113ARGARGSERSER(chain 'F' and ((resid 445 and (name N or name...FF445 - 4492 - 6
2123ARGARGSERSERchain 'G'GG445 - 4492 - 6

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
14-3-3 protein gamma / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27004.426 Da / Num. of mol.: 4 / Mutation: S235Stop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61981
#2: Protein/peptide
E3 ubiquitin-protein ligase NEDD4-like / HECT-type E3 ubiquitin transferase NED4L / NEDD4.2 / Nedd4-2


Mass: 1125.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96PU5, HECT-type E3 ubiquitin transferase
#3: Chemical
ChemComp-CFH / 1,1,1,3,3,3-hexafluoropropan-2-ol


Mass: 168.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2F6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 19, 2019 / Details: Sagitally bended Si111 crystal
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.89895988606→25.7722546026 Å / Num. obs: 92751 / % possible obs: 99.76 % / Redundancy: 5.84 % / Biso Wilson estimate: 39.5909253364 Å2 / Rrim(I) all: 0.051 / Net I/σ(I): 20.39
Reflection shellResolution: 1.899→1.967 Å / Num. unique obs: 9202 / Rrim(I) all: 1.038

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B05

2b05


Resolution: 1.89895988606→25.7722546026 Å / SU ML: 0.292331465261 / Cross valid method: FREE R-VALUE / σ(F): 1.92414449541 / Phase error: 29.3358275781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239347564833 2099 2.26351205625 %
Rwork0.211915834691 90633 -
obs0.212551383511 92732 99.7815677624 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.8045996391 Å2
Refinement stepCycle: LAST / Resolution: 1.89895988606→25.7722546026 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 40 551 7984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003658566712427536
X-RAY DIFFRACTIONf_angle_d0.60785923584810203
X-RAY DIFFRACTIONf_chiral_restr0.03826036878141151
X-RAY DIFFRACTIONf_plane_restr0.003183246009131303
X-RAY DIFFRACTIONf_dihedral_angle_d7.481065396864639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.94310.4217510054171370.4025133897725890X-RAY DIFFRACTION98.127645718
1.9431-1.99170.3320582675981400.3298280480766082X-RAY DIFFRACTION99.8555609052
1.9917-2.04550.3433388842071410.2988581825496059X-RAY DIFFRACTION99.8872241018
2.0455-2.10570.320172884541390.2761541839986020X-RAY DIFFRACTION99.8055420515
2.1057-2.17360.3019125923331410.2421731612586071X-RAY DIFFRACTION99.9356499356
2.1736-2.25130.2673823312571400.2336362474496061X-RAY DIFFRACTION99.8711547753
2.2513-2.34130.2595348278641400.2237700443996050X-RAY DIFFRACTION99.9838475206
2.3413-2.44780.2875886949531400.2224753953146044X-RAY DIFFRACTION99.9676689298
2.4478-2.57680.2673201444231410.2262079825236083X-RAY DIFFRACTION99.9036918138
2.5768-2.7380.2384565537911400.2279740059446033X-RAY DIFFRACTION99.9352436458
2.738-2.94920.3070719677311390.2310999177916027X-RAY DIFFRACTION99.902786779
2.9492-3.24540.2263887566781400.2263887566786059X-RAY DIFFRACTION99.9355150734
3.2454-3.71390.2121502519081410.2048207509586055X-RAY DIFFRACTION99.9838631596
3.7139-4.67450.187456113091400.1735860118666074X-RAY DIFFRACTION99.9839098954
4.6745-25.77225460260.2221572596451400.1843777189646025X-RAY DIFFRACTION99.6927554981

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