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- PDB-2xbf: Nedd4 HECT structure -

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Basic information

Entry
Database: PDB / ID: 2xbf
TitleNedd4 HECT structure
ComponentsE3 UBIQUITIN-PROTEIN LIGASE NEDD4
KeywordsLIGASE
Function / homology
Function and homology information


formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / channel inhibitor activity / nuclear receptor-mediated glucocorticoid signaling pathway / viral budding / negative regulation of potassium ion export across plasma membrane / endocardial cushion development / phosphothreonine residue binding / receptor catabolic process ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / channel inhibitor activity / nuclear receptor-mediated glucocorticoid signaling pathway / viral budding / negative regulation of potassium ion export across plasma membrane / endocardial cushion development / phosphothreonine residue binding / receptor catabolic process / apicolateral plasma membrane / protein targeting to lysosome / potassium channel inhibitor activity / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / proline-rich region binding / RNA polymerase binding / blood vessel morphogenesis / beta-2 adrenergic receptor binding / lysosomal transport / regulation of dendrite morphogenesis / negative regulation of vascular endothelial growth factor receptor signaling pathway / sodium ion transport / neuromuscular junction development / regulation of synapse organization / outflow tract morphogenesis / protein K63-linked ubiquitination / phosphoserine residue binding / protein monoubiquitination / regulation of macroautophagy / ubiquitin ligase complex / postsynaptic cytosol / progesterone receptor signaling pathway / ionotropic glutamate receptor binding / Downregulation of ERBB4 signaling / Regulation of PTEN localization / T cell activation / ubiquitin binding / regulation of membrane potential / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / neuron projection development / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / cell cortex / adaptive immune response / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / protein domain specific binding / innate immune response / DNA damage response / chromatin / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) ...Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsMaspero, E. / Cecatiello, V. / Musacchio, A. / Polo, S. / Pasqualato, S.
CitationJournal: Embo Rep. / Year: 2011
Title: Structure of the Hect:Ubiquitin Complex and its Role in Ubiquitin Chain Elongation
Authors: Maspero, E. / Mari, S. / Valentini, E. / Musacchio, A. / Fish, A. / Pasqualato, S. / Polo, S.
History
DepositionApr 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE NEDD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0706
Polymers45,7821
Non-polymers2885
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.405, 38.843, 60.640
Angle α, β, γ (deg.)90.00, 93.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE NEDD4 / NEDD-4 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 4 / CELL ...NEDD-4 / NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 4 / CELL PROLIFERATION-INDUCING GENE 53 PROTEIN


Mass: 45782.109 Da / Num. of mol.: 1 / Fragment: HECT DOMAIN, RESIDUES 519-900
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P46934, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsISOFORM 4 P46934-4

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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 % / Description: NONE
Crystal growpH: 6
Details: 100 MM NA-MES, PH 6.0, 4% PEG 400, 35 MM CACL2, 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14288 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34.57 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.3 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ONI

2oni


Resolution: 2.503→48.576 Å / SU ML: 1.21 / σ(F): 1.35 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 705 4.9 %
Rwork0.1968 --
obs0.1997 14282 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.784 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9601 Å2-0 Å20.2569 Å2
2---2.2981 Å20 Å2
3---0.3379 Å2
Refinement stepCycle: LAST / Resolution: 2.503→48.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 17 197 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033278
X-RAY DIFFRACTIONf_angle_d0.6034415
X-RAY DIFFRACTIONf_dihedral_angle_d16.3811206
X-RAY DIFFRACTIONf_chiral_restr0.047443
X-RAY DIFFRACTIONf_plane_restr0.002570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5034-2.69660.31121500.2412541X-RAY DIFFRACTION94
2.6966-2.9680.31661310.23032729X-RAY DIFFRACTION100
2.968-3.39740.2551340.2062730X-RAY DIFFRACTION100
3.3974-4.27990.22781600.16412739X-RAY DIFFRACTION100
4.2799-48.58550.22411300.17412838X-RAY DIFFRACTION100

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