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- PDB-4be8: NEDD4 HECT A889F structure -

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Basic information

Entry
Database: PDB / ID: 4be8
TitleNEDD4 HECT A889F 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 / regulation of potassium ion transmembrane transporter activity / viral budding / nuclear receptor-mediated glucocorticoid signaling pathway / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome ...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 / negative regulation of sodium ion transmembrane transporter activity / phosphothreonine residue binding / receptor catabolic process / protein targeting to lysosome / apicolateral plasma membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / HECT-type E3 ubiquitin transferase / sodium channel inhibitor activity / proline-rich region binding / regulation of monoatomic ion transmembrane transport / RNA polymerase binding / lysosomal transport / neuromuscular junction development / regulation of dendrite morphogenesis / regulation of synapse organization / negative regulation of vascular endothelial growth factor receptor signaling pathway / progesterone receptor signaling pathway / protein K63-linked ubiquitination / phosphoserine residue binding / regulation of macroautophagy / beta-2 adrenergic receptor binding / ubiquitin ligase complex / 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 / cellular response to UV / neuron projection development / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell cortex / ubiquitin-dependent protein catabolic process / dendritic spine / 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 / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / Hect, E3 ligase catalytic fold / Hect, E3 ligase catalytic domain / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. ...Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domain / Hect, E3 ligase catalytic domains / Hect, E3 ligase catalytic domain fold / 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: 2.996 Å
AuthorsMaspero, E. / Valentini, E. / Mari, S. / Cecatiello, V. / Polo, S. / Pasqualato, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of a Ubiquitin-Loaded Hect Ligase Reveals the Molecular Basis for Catalytic Priming
Authors: Maspero, E. / Valentini, E. / Mari, S. / Cecatiello, V. / Soffientini, P. / Pasqualato, S. / Polo, S.
History
DepositionMar 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Aug 28, 2013Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)45,7071
Polymers45,7071
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.545, 100.545, 96.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 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: 45707.000 Da / Num. of mol.: 1 / Fragment: HECT DOMAIN, RESIDUES 519-900 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.7 Å3/Da / Density % sol: 54.5 % / Description: NONE
Crystal growpH: 9
Details: 1.15 M POTASSIUM SODIUM TARTRATE, 0.1 M TRIS-HCL, PH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→44.58 Å / Num. obs: 11622 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 84.83 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XBB

2xbb


Resolution: 2.996→44.58 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 38.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 581 5 %
Rwork0.2457 --
obs0.2482 11550 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 136.4 Å2
Refinement stepCycle: LAST / Resolution: 2.996→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 0 3 3124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033207
X-RAY DIFFRACTIONf_angle_d0.7874331
X-RAY DIFFRACTIONf_dihedral_angle_d13.1031179
X-RAY DIFFRACTIONf_chiral_restr0.061442
X-RAY DIFFRACTIONf_plane_restr0.004559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9963-3.29780.41861440.37882691X-RAY DIFFRACTION99
3.2978-3.77480.39981410.32852703X-RAY DIFFRACTION98
3.7748-4.75490.28531440.23852702X-RAY DIFFRACTION98
4.7549-44.58510.24791520.20262873X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5601-0.5011-1.03773.17270.76533.31820.0699-0.1487-0.05990.02160.2949-0.8750.40820.6865-0.25621.01660.0583-0.07881.1672-0.11181.077-35.007819.55468.9207
23.2411-1.5773-0.6172.02430.37181.73050.04970.65470.1101-0.3637-0.33060.3173-0.3126-0.6590.06621.0610.1011-0.07281.985-0.10591.143-67.671433.11197.186
32.0827-0.08540.62993.20720.36972.52870.0541-0.0731-0.05630.45240.0795-0.33690.1120.2191-0.11470.99080.0943-0.0081.0830.06950.9134-42.247525.888714.2904
42.09720.09170.46534.3866-0.12892.8103-0.05580.27410.1994-0.31530.06840.11530.02160.021-0.01980.7579-0.122-0.0261.0817-0.00691.0071-41.775450.09815.1612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 517 THROUGH 669 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 670 THROUGH 739 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 740 THROUGH 783 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 784 THROUGH 894 )

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