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- PDB-4n7f: Crystal structure of 3rd WW domain of human Nedd4-1 -

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Basic information

Entry
Database: PDB / ID: 4n7f
TitleCrystal structure of 3rd WW domain of human Nedd4-1
ComponentsE3 ubiquitin-protein ligase NEDD4
KeywordsPROTEIN BINDING / beta sheet / WW domain / target binding / proline rich region / cytosolic
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 / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / : / phosphothreonine residue binding / receptor catabolic process / apicolateral plasma membrane ...formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / : / phosphothreonine residue binding / receptor catabolic process / apicolateral plasma membrane / protein targeting to lysosome / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / proline-rich region binding / sodium channel inhibitor activity / RNA polymerase binding / beta-2 adrenergic receptor binding / lysosomal transport / regulation of dendrite morphogenesis / neuromuscular junction development / negative regulation of vascular endothelial growth factor receptor signaling pathway / regulation of synapse organization / phosphoserine residue binding / protein K63-linked ubiquitination / ubiquitin ligase complex / regulation of macroautophagy / progesterone receptor signaling pathway / Downregulation of ERBB4 signaling / Regulation of PTEN localization / ubiquitin binding / regulation of membrane potential / receptor internalization / ISG15 antiviral mechanism / Regulation of PTEN stability and activity / response to calcium ion / positive regulation of protein catabolic process / neuron projection development / ubiquitin-protein transferase activity / cellular response to UV / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / 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 / 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 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. ...: / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase NEDD4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.102 Å
AuthorsQi, S. / O'Hayre, M. / Gutkind, J.S. / Hurley, J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and biochemical basis for ubiquitin ligase recruitment by arrestin-related domain-containing protein-3 (ARRDC3).
Authors: Qi, S. / O'Hayre, M. / Gutkind, J.S. / Hurley, J.H.
History
DepositionOct 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase NEDD4
B: E3 ubiquitin-protein ligase NEDD4


Theoretical massNumber of molelcules
Total (without water)8,8942
Polymers8,8942
Non-polymers00
Water1,910106
1
A: E3 ubiquitin-protein ligase NEDD4


Theoretical massNumber of molelcules
Total (without water)4,4471
Polymers4,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase NEDD4


Theoretical massNumber of molelcules
Total (without water)4,4471
Polymers4,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.411, 68.411, 37.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-436-

ARG

21B-436-

ARG

31B-436-

ARG

41A-524-

HOH

51A-528-

HOH

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4 / Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down- ...Cell proliferation-inducing gene 53 protein / Neural precursor cell expressed developmentally down-regulated protein 4 / NEDD-4


Mass: 4447.042 Da / Num. of mol.: 2 / Fragment: WW3 domain (UNP residues 841-874)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0093, NEDD4, NEDD4-1, PIG53 / Plasmid: pGST-parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46934
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3.0M NaCl, 100mM Tris-HCl 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→32.7 Å / Num. all: 36280 / Num. obs: 36262 / % possible obs: 95 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.1-1.14198.9
1.14-1.181100
1.18-1.241100
1.24-1.31100
1.3-1.391100
1.39-1.491100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.102→32.713 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8829 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1806 4.99 %
Rwork0.1812 34404 -
obs0.1822 36210 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.74 Å2 / Biso mean: 27.4254 Å2 / Biso min: 8.28 Å2
Refinement stepCycle: LAST / Resolution: 1.102→32.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 0 106 716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01657
X-RAY DIFFRACTIONf_angle_d1.403895
X-RAY DIFFRACTIONf_chiral_restr0.06387
X-RAY DIFFRACTIONf_plane_restr0.009117
X-RAY DIFFRACTIONf_dihedral_angle_d10.869243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1019-1.13170.21331150.20092584269999
1.1317-1.1650.1781360.186626092745100
1.165-1.20260.19941410.188625882729100
1.2026-1.24560.24141430.189626032746100
1.2456-1.29550.23851250.191326292754100
1.2955-1.35450.23641470.179925912738100
1.3545-1.42590.19761330.176826462779100
1.4259-1.51520.18211350.184126122747100
1.5152-1.63220.22391330.173926572790100
1.6322-1.79640.23481580.172126292787100
1.7964-2.05630.17221480.163626722820100
2.0563-2.59060.19581420.176427172859100
2.5906-32.72770.1941500.190728673017100

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