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- PDB-7lp1: Structure of Nedd4L WW3 domain -

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Basic information

Entry
Database: PDB / ID: 7lp1
TitleStructure of Nedd4L WW3 domain
ComponentsE3 ubiquitin-protein ligase NEDD4-like
KeywordsLIGASE / PPxY binding / E3 Ubiquitin ligase / Nedd4L
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 potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization ...positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport / regulation of sodium ion transmembrane transport / negative regulation of sodium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / regulation of membrane repolarization / positive regulation of dendrite extension / HECT-type E3 ubiquitin transferase / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / regulation of dendrite morphogenesis / regulation of membrane depolarization / protein monoubiquitination / sodium channel regulator activity / protein K48-linked ubiquitination / potassium channel regulator activity / regulation of membrane potential / multivesicular body / monoatomic ion transmembrane transport / Downregulation of TGF-beta receptor signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / regulation of protein stability / Budding and maturation of HIV virion / Stimuli-sensing channels / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / cell differentiation / protein ubiquitination / Golgi apparatus / extracellular exosome / nucleoplasm / cytosol / cytoplasm
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 / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...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 / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
NITRATE ION / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsAlian, A. / Alam, S.L. / Thompson, T. / Rheinemann, L. / Sundquist, W.I.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Interactions between AMOT PPxY motifs and NEDD4L WW domains function in HIV-1 release.
Authors: Rheinemann, L. / Thompson, T. / Mercenne, G. / Paine, E.L. / Peterson, F.C. / Volkman, B.F. / Alam, S.L. / Alian, A. / Sundquist, W.I.
History
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / software

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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-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0086
Polymers4,6381
Non-polymers3705
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.344, 40.344, 54.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase NEDD4-like / HECT-type E3 ubiquitin transferase NED4L / NEDD4.2 / Nedd4-2


Mass: 4638.264 Da / Num. of mol.: 1 / Fragment: WW 3 domain, residues 494-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L, KIAA0439, NEDL3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q96PU5, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.6M ammonium nitrate, 5% glycerol, and 0.1M sodium acetate at pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1→50 Å / Num. obs: 11774 / % possible obs: 99.83 % / Redundancy: 2 % / Biso Wilson estimate: 13 Å2 / CC1/2: 1 / Net I/σ(I): 33.25
Reflection shellResolution: 1.35→1.398 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1685 / Mean I/σ(I) obs: 4.26 / Num. unique obs: 1140 / CC1/2: 0.958 / Rrim(I) all: 0.2383 / % possible all: 98.16

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2mpt

2mpt


Resolution: 1.35→29.47 Å / SU ML: 0.095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 1185 10.07 %
Rwork0.1836 10586 -
obs0.1868 11771 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.39 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms328 0 24 45 397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01360
X-RAY DIFFRACTIONf_angle_d1.1162484
X-RAY DIFFRACTIONf_chiral_restr0.077147
X-RAY DIFFRACTIONf_plane_restr0.00863
X-RAY DIFFRACTIONf_dihedral_angle_d7.752945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.410.26481410.22311281X-RAY DIFFRACTION98.27
1.41-1.490.2111460.19911307X-RAY DIFFRACTION100
1.49-1.580.22181400.19521299X-RAY DIFFRACTION99.93
1.58-1.70.20311430.17521318X-RAY DIFFRACTION100
1.7-1.870.20791450.19121302X-RAY DIFFRACTION99.93
1.87-2.140.19351520.17291330X-RAY DIFFRACTION100
2.14-2.70.2151540.18471337X-RAY DIFFRACTION100
2.7-29.470.21771640.17931412X-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)
16.67189898093-5.27428124337-1.199439079687.052825136680.4750064530052.14757489762-0.07062628002120.0312066924399-0.1360177462560.1338285026140.06421717997010.150579885380.488496430771-0.139107668943-0.0316444273660.0789900069235-0.0136108530610.00272698206090.11916121039-0.0130554391680.0883239107635-25.962320149510.052164509-3.11032051683
24.764624117612.871309913191.012530521552.78868471714-2.216257506137.764442818480.150332481331-0.687664490631-0.7196662551890.5320330680130.05621719502560.4878216842340.552687186559-0.323743854685-0.1025973343140.184815145360.07498172874470.01025797458390.2393580004290.04450170748620.223546914156-30.22047954969.458565685926.69116300642
31.005454958741.314552562030.4353982664832.641835292651.000313650890.390591307129-0.141237878694-0.1449218806810.5281811197480.262034790886-0.09346936769290.194958985522-0.763320026141-0.4961795802660.2503333524110.3237834495040.148848099896-0.0271686328150.202215978072-0.03774331621050.143813035293-23.58690255616.086535652211.867813949
45.68585433251-1.401337649981.590254353764.43684391251-2.624550580814.86040411249-0.241934846549-0.02871562148890.3507410870650.203520849097-0.0782079649555-0.369866172029-0.1915595444990.1429696029920.1961810514560.0962653630170.0116836843475-0.01788229747250.1072146110170.00858533051270.0826137666349-21.042173975815.99147916030.789332440943
52.64785428181-2.294030727060.8685049683265.979995004-1.911952080685.230247160540.06147727818980.178062909824-0.0329195113762-0.125722677571-0.177890613553-0.01582383288290.2338790080830.1660826681980.1081306305730.06592739605930.01364230813650.004644097003370.123024910896-0.008690011476740.0609270786318-21.733854471613.177584892-3.09714935355
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 522 through 527 )522 - 52729 - 34
22chain 'A' and (resid 528 through 532 )528 - 53235 - 39
33chain 'A' and (resid 494 through 502 )494 - 5021 - 9
44chain 'A' and (resid 503 through 507 )503 - 50710 - 14
55chain 'A' and (resid 508 through 521 )508 - 52115 - 28

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