[English] 日本語
Yorodumi
- PDB-6zbt: Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zbt
TitleStructure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342
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


positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / positive regulation of cell-cell adhesion / negative regulation of protein localization to cell surface / phosphorylation-dependent protein binding / positive regulation of dendrite extension ...positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of sodium ion import across plasma membrane / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / positive regulation of cell-cell adhesion / negative regulation of protein localization to cell surface / phosphorylation-dependent protein binding / positive regulation of dendrite extension / regulation of membrane repolarization / regulation of membrane depolarization / receptor catabolic process / regulation of sodium ion transmembrane transport / potassium channel inhibitor activity / positive regulation of T cell mediated immune response to tumor cell / ventricular cardiac muscle cell action potential / 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 / protein targeting / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein K48-linked ubiquitination / negative regulation of protein kinase activity / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / 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 / protein kinase C binding / Downregulation of TGF-beta receptor signaling / AURKA Activation by TPX2 / regulation of membrane potential / TP53 Regulates Metabolic Genes / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Budding and maturation of HIV virion / receptor tyrosine kinase binding / regulation of synaptic plasticity / positive regulation of T cell activation / regulation of protein stability / receptor internalization / Stimuli-sensing channels / cellular response to insulin stimulus / neuron projection development / positive regulation of protein catabolic process / 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 / apical plasma membrane / mitochondrial matrix / protein domain specific binding / focal adhesion / Golgi apparatus / signal transduction / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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 / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / 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: 1.799485197 Å
AuthorsJoshi, R. / 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 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)113,21512
Polymers112,5428
Non-polymers6724
Water11,566642
1
A: 14-3-3 protein gamma
B: 14-3-3 protein gamma
E: E3 ubiquitin-protein ligase NEDD4-like
G: E3 ubiquitin-protein ligase NEDD4-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7757
Polymers56,2714
Non-polymers5043
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-28 kcal/mol
Surface area22760 Å2
MethodPISA
2
C: 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)56,4395
Polymers56,2714
Non-polymers1681
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-28 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.857, 205.857, 74.354
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

-
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: 1131.175 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.: 642 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol

-
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: 1.799→27.5102551593 Å / Num. obs: 108872 / % possible obs: 99.88 % / Redundancy: 5.81 % / Biso Wilson estimate: 31.6177163868 Å2 / Rrim(I) all: 0.041 / Net I/σ(I): 25.82
Reflection shellResolution: 1.799→1.864 Å / Num. unique obs: 10874 / Rrim(I) all: 0.597

-
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: 1.799485197→27.5102551593 Å / SU ML: 0.239143595933 / Cross valid method: FREE R-VALUE / σ(F): 1.92845296366 / Phase error: 26.8248386407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.240503098065 2099 1.92821775357 %
Rwork0.210094799993 106758 -
obs0.210674554238 108857 99.9091376335 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.2003851277 Å2
Refinement stepCycle: LAST / Resolution: 1.799485197→27.5102551593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7332 0 40 642 8014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002827615157717470
X-RAY DIFFRACTIONf_angle_d0.50499246372910121
X-RAY DIFFRACTIONf_chiral_restr0.03329757098891160
X-RAY DIFFRACTIONf_plane_restr0.002747297562721283
X-RAY DIFFRACTIONf_dihedral_angle_d7.864831326274583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7995-1.84130.3296125064371400.306463847947117X-RAY DIFFRACTION99.4927337538
1.8413-1.88740.3138718547851400.2757247752597103X-RAY DIFFRACTION99.972394755
1.8874-1.93840.3201705698851390.2660980547387093X-RAY DIFFRACTION100
1.9384-1.99540.3024590125021400.2639000492497117X-RAY DIFFRACTION99.931148444
1.9954-2.05980.2608726016141400.2471742434897106X-RAY DIFFRACTION99.972406181
2.0598-2.13340.2830653878651400.2344783431877181X-RAY DIFFRACTION99.9181110959
2.1334-2.21880.2800452271081390.2300824488327064X-RAY DIFFRACTION99.9306326304
2.2188-2.31970.2505181870751410.2243291455257133X-RAY DIFFRACTION99.9862542955
2.3197-2.44190.2771667771191400.2248058385287137X-RAY DIFFRACTION99.9725236983
2.4419-2.59480.2328282111541390.2193457325167095X-RAY DIFFRACTION99.9861782999
2.5948-2.7950.2368543186091410.2205137418617131X-RAY DIFFRACTION99.9038329441
2.795-3.07590.2670511026221400.2233096418287124X-RAY DIFFRACTION99.9862353751
3.0759-3.52020.2461905401861400.210702242667133X-RAY DIFFRACTION99.9587685542
3.5202-4.43210.1965671051231400.1753654686067119X-RAY DIFFRACTION100
4.4321-27.51025515930.2090219944781400.1848769838127105X-RAY DIFFRACTION99.6698307883

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more