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- PDB-7lp3: Structure of Nedd4L WW3 domain -

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Basic information

Entry
Database: PDB / ID: 7lp3
TitleStructure of Nedd4L WW3 domain
Components
  • Angiomotin
  • E3 ubiquitin-protein ligase NEDD4-like
KeywordsLIGASE / PPxY binding / E3 Ubiquitin ligase / Nedd4L
Function / homology
Function and homology information


establishment of cell polarity involved in ameboidal cell migration / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / cell migration involved in gastrulation / blood vessel endothelial cell migration / negative regulation of sodium ion import across plasma membrane / Regulation of CDH11 function / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport ...establishment of cell polarity involved in ameboidal cell migration / positive regulation of caveolin-mediated endocytosis / RING-type E3 ubiquitin transferase (cysteine targeting) / negative regulation of sodium ion transmembrane transport / cell migration involved in gastrulation / blood vessel endothelial cell migration / negative regulation of sodium ion import across plasma membrane / Regulation of CDH11 function / negative regulation of potassium ion export across plasma membrane / negative regulation of potassium ion transmembrane transport / positive regulation of embryonic development / negative regulation of protein localization to cell surface / angiostatin binding / positive regulation of dendrite extension / regulation of membrane repolarization / regulation of membrane depolarization / receptor catabolic process / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / regulation of sodium ion transmembrane transport / potassium channel inhibitor activity / ventricular cardiac muscle cell action potential / HECT-type E3 ubiquitin transferase / gastrulation with mouth forming second / negative regulation of vascular permeability / sodium channel inhibitor activity / cell-cell junction assembly / Signaling by Hippo / regulation of small GTPase mediated signal transduction / regulation of dendrite morphogenesis / neuromuscular junction development / regulation of synapse organization / sodium channel regulator activity / endocytic vesicle / positive regulation of blood vessel endothelial cell migration / positive regulation of cell size / protein monoubiquitination / bicellular tight junction / vasculogenesis / protein K48-linked ubiquitination / stress fiber / positive regulation of stress fiber assembly / ruffle / multivesicular body / regulation of cell migration / negative regulation of angiogenesis / Downregulation of TGF-beta receptor signaling / regulation of membrane potential / actin filament / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Budding and maturation of HIV virion / regulation of protein stability / receptor internalization / Stimuli-sensing channels / chemotaxis / neuron projection development / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / intracellular protein localization / Antigen processing: Ubiquitination & Proteasome degradation / signaling receptor activity / lamellipodium / actin cytoskeleton organization / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / monoatomic ion transmembrane transport / angiogenesis / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / postsynaptic density / protein ubiquitination / apical plasma membrane / external side of plasma membrane / glutamatergic synapse / cell surface / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. ...Angiomotin / Angiomotin, C-terminal / : / Angiomotin C terminal / 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 / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / C2 domain / WW/rsp5/WWP domain signature. / 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
Angiomotin / E3 ubiquitin-protein ligase NEDD4-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 / pdbx_initial_refinement_model

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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
B: Angiomotin
C: E3 ubiquitin-protein ligase NEDD4-like
D: Angiomotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5668
Polymers12,1824
Non-polymers3844
Water1,72996
1
A: E3 ubiquitin-protein ligase NEDD4-like
B: Angiomotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2834
Polymers6,0912
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-35 kcal/mol
Surface area4080 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase NEDD4-like
D: Angiomotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2834
Polymers6,0912
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-35 kcal/mol
Surface area4120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.565, 55.522, 82.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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: 4445.951 Da / Num. of mol.: 2 / Fragment: WW 1 domain, residues 193-226
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: Protein/peptide Angiomotin


Mass: 1644.869 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop
Details: 1.6M (NH4)2SO4, 0.1M Potassium Sodium Tartrate, 5% glycerol, 0.1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.61→23.04 Å / Num. obs: 18091 / % possible obs: 99.19 % / Redundancy: 2 % / Biso Wilson estimate: 12.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0399 / Rrim(I) all: 0.0564 / Net I/σ(I): 7.05
Reflection shellResolution: 1.52→1.575 Å / Redundancy: 2 % / Rmerge(I) obs: 0.6143 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1756 / CC1/2: 0.62 / Rrim(I) all: 0.8688 / % possible all: 96.03

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Processing

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

2mpt


Resolution: 1.61→23.04 Å / SU ML: 0.1513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8165
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2097 1527 10 %
Rwork0.1779 13736 -
obs0.1811 15263 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.41 Å2
Refinement stepCycle: LAST / Resolution: 1.61→23.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 20 98 978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097916
X-RAY DIFFRACTIONf_angle_d1.11621254
X-RAY DIFFRACTIONf_chiral_restr0.0594110
X-RAY DIFFRACTIONf_plane_restr0.0093166
X-RAY DIFFRACTIONf_dihedral_angle_d5.9725114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.660.25961350.22651218X-RAY DIFFRACTION99.63
1.66-1.720.29991360.2141225X-RAY DIFFRACTION99.93
1.72-1.790.24281380.19071229X-RAY DIFFRACTION99.49
1.79-1.870.19811360.19151230X-RAY DIFFRACTION99.93
1.87-1.970.1951360.17891223X-RAY DIFFRACTION99.56
1.97-2.090.20341380.17071243X-RAY DIFFRACTION99.78
2.09-2.260.21341390.15191242X-RAY DIFFRACTION99.86
2.26-2.480.21181390.17381235X-RAY DIFFRACTION99.42
2.48-2.840.1961390.17331255X-RAY DIFFRACTION99.64
2.84-3.570.19551420.16911288X-RAY DIFFRACTION99.51
3.58-24.660.20491490.1811348X-RAY DIFFRACTION99.01
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)
17.5106562140.5670439463351.012749633172.71444995212-2.305734139465.489897927060.01498920694460.145603176552-0.977392101855-0.2704284804260.1414248720560.5526109985870.652210732079-0.9380039606170.06143503307440.216717667765-0.02037577041810.02561683927620.324652704317-0.08561349061580.25138397251-17.183918384117.2606536923-6.10628323121
21.20454714548-0.01599185071970.7599515566723.791081957422.060710270413.35936398851-0.01479955406070.213154449401-0.2659994964580.121851892947-0.02661966897870.1522015817510.120398466274-0.1840391080130.04399924992030.0655326253007-0.006531550489560.0125934401350.110209914814-0.04760738966060.0938554642245-6.3432703125917.7480944337-11.0861642581
31.11513459489-0.6844475556690.2777908037031.584929435330.02152073927331.706007829110.1630460493340.395549908192-0.2163634821120.102436923052-0.151381778476-0.5706597239240.169437190131-0.0359472939418-0.1371604476080.0763097318067-0.004000603534730.009825723488380.174625696079-0.06719013295510.1630767519851.0117600745217.8466289443-14.3838082143
44.414467969433.87709553681-2.988888881645.10528135544-3.767376893846.128103991190.1578568811240.2125089548820.6438141028870.0879568142453-0.293222400346-0.356050211827-0.2616575056230.9001385971580.02243650915470.184154961429-0.0146130048621-0.008697162591210.2657317678380.06068528705350.2430844575964.8961203162537.7609665048-6.48594089127
51.61536897767-1.221682432481.56835180584.85840392156-4.361415034555.597622151580.09046665480380.3848890406520.166932350712-0.1343926021020.0611923325830.2997041263730.0833699579087-0.0889926613503-0.07620880121950.0894527388829-0.002966955146260.01207953528940.1731900465480.06899737322720.139325679481-5.0680378535737.4243270197-17.1875400004
62.376680339590.426568420099-0.2578583836273.09574842825-0.7856903951721.970959757860.0131228142579-0.0503826678720.08407315180320.366403787384-0.0704085927117-0.2339558581-0.1965517591880.1346017453120.04189655696390.08694726388320.0142642300266-0.01890165093790.09110157657680.03763793281350.0850901486744-6.3978097531737.0448367079-8.34030122941
71.68702254334-0.675679737882-0.677043141395.75433575277-2.642809768372.577106272180.04326086446530.5657633810310.2544919130080.08633237125530.07072057469990.749234383809-0.228406828615-0.0284293611499-0.2197030762270.0805901197818-0.00281103194675-0.03295007908570.183247345440.08890259629060.175534232251-13.354228812136.95928205-14.7794965242
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -3 through 198 )AA-3 - 1981 - 9
22chain 'A' and (resid 199 through 226 )AA199 - 22610 - 37
33chain 'B' and (resid 234 through 247 )BB234 - 2471 - 14
44chain 'C' and (resid -3 through 198 )CC-3 - 1981 - 9
55chain 'C' and (resid 199 through 208 )CC199 - 20810 - 19
66chain 'C' and (resid 209 through 226 )CC209 - 22620 - 37
77chain 'D' and (resid 234 through 247 )DD234 - 2471 - 14

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