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- PDB-4n7h: Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 ... -

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Basic information

Entry
Database: PDB / ID: 4n7h
TitleCrystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of ARRDC3
Components
  • Arrestin domain-containing protein 3
  • E3 ubiquitin-protein ligase NEDD4
KeywordsPROTEIN BINDING / ww domain / Beta sheet / PPXY motif
Function / homology
Function and homology information


negative regulation of heat generation / beta-3 adrenergic receptor binding / formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of locomotion involved in locomotory behavior / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway ...negative regulation of heat generation / beta-3 adrenergic receptor binding / formation of structure involved in a symbiotic process / positive regulation of nucleocytoplasmic transport / negative regulation of locomotion involved in locomotory behavior / negative regulation of sodium ion transport / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of hippo signaling / : / 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 / heat generation / beta-2 adrenergic receptor binding / negative regulation of cold-induced thermogenesis / positive regulation of ubiquitin-protein transferase activity / lysosomal transport / fat pad development / regulation of dendrite morphogenesis / neuromuscular junction development / negative regulation of vascular endothelial growth factor receptor signaling pathway / skin development / 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 / protein transport / cell cortex / ubiquitin-dependent protein catabolic process / early endosome / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / 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
: / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / : / Arrestin-like, C-terminal / HECT domain / HECT, E3 ligase catalytic domain ...: / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / : / Arrestin-like, C-terminal / 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 / Immunoglobulin E-set
Similarity search - Domain/homology
GUANIDINE / E3 ubiquitin-protein ligase NEDD4 / Arrestin domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.698 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
B: Arrestin domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7964
Polymers5,6782
Non-polymers1182
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-5 kcal/mol
Surface area3280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.882, 38.882, 49.997
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-501-

GAI

21A-501-

GAI

31A-615-

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: 4261.756 Da / Num. of mol.: 1 / Fragment: 3rd WW domain (UNP residues 840-872)
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: Protein/peptide Arrestin domain-containing protein 3 / TBP-2-like inducible membrane protein / TLIMP


Mass: 1416.554 Da / Num. of mol.: 1 / Fragment: 1st PPXY Motif (UNP residues 342-354) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96B67
#3: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.35M (NH4)SO4, 100mM Tris-HCl 8.0, 100mM Guanidine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / 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: 1.7→50 Å / Num. obs: 5129 / % possible obs: 99.6 % / Redundancy: 13.3 % / Biso Wilson estimate: 26.01 Å2 / Rmerge(I) obs: 0.068 / Χ2: 1.178 / Net I/σ(I): 24.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7611.10.215081.233199.4
1.76-1.8313.40.1744851.201199.8
1.83-1.91140.1455141.2231100
1.91-2.0213.90.1184981.2421100
2.02-2.1414.10.1055061.2181100
2.14-2.3113.80.0984991.1341100
2.31-2.54140.0935161.1131100
2.54-2.9113.80.0815161.149199.8
2.91-3.6613.40.0635251.105199.6
3.66-5011.80.0555621.179197.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.698→33.673 Å / Occupancy max: 1 / Occupancy min: 0.51 / FOM work R set: 0.7813 / SU ML: 0.19 / σ(F): 1.37 / Phase error: 26.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 235 4.6 %
Rwork0.1888 4874 -
obs0.1907 5109 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.13 Å2 / Biso mean: 29.4486 Å2 / Biso min: 16.58 Å2
Refinement stepCycle: LAST / Resolution: 1.698→33.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms346 0 8 31 385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011366
X-RAY DIFFRACTIONf_angle_d1.291498
X-RAY DIFFRACTIONf_chiral_restr0.04947
X-RAY DIFFRACTIONf_plane_restr0.00868
X-RAY DIFFRACTIONf_dihedral_angle_d15.743130
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6983-2.13960.26631120.193323952507100
2.1396-33.67940.22491230.18772479260299

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