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- PDB-7lp2: Structure of Nedd4L WW3 domain -

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Basic information

Entry
Database: PDB / ID: 7lp2
TitleStructure of Nedd4L WW3 domain
Components
  • Angiomotin
  • E3 ubiquitin-protein ligase
KeywordsLIGASE / WW domain / PPxY binding / E3 Ubiquitin ligase / Nedd4L
Function / homology
Function and homology information


establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / blood vessel endothelial cell migration / Regulation of CDH11 function / positive regulation of embryonic development / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / HECT-type E3 ubiquitin transferase / gastrulation with mouth forming second ...establishment of cell polarity involved in ameboidal cell migration / cell migration involved in gastrulation / blood vessel endothelial cell migration / Regulation of CDH11 function / positive regulation of embryonic development / angiostatin binding / regulation of modification of postsynaptic actin cytoskeleton / hippo signaling / HECT-type E3 ubiquitin transferase / gastrulation with mouth forming second / negative regulation of vascular permeability / cell-cell junction assembly / Signaling by Hippo / regulation of small GTPase mediated signal transduction / endocytic vesicle / positive regulation of blood vessel endothelial cell migration / positive regulation of cell size / bicellular tight junction / vasculogenesis / stress fiber / positive regulation of stress fiber assembly / ruffle / regulation of cell migration / negative regulation of angiogenesis / actin filament / chemotaxis / ubiquitin protein ligase activity / intracellular protein localization / signaling receptor activity / lamellipodium / actin cytoskeleton organization / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / angiogenesis / in utero embryonic development / postsynaptic density / protein ubiquitination / external side of plasma membrane / glutamatergic synapse / cell surface / negative regulation of transcription by RNA polymerase II / 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
E3 ubiquitin-protein ligase / Angiomotin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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
B: Angiomotin
C: E3 ubiquitin-protein ligase
D: Angiomotin
E: E3 ubiquitin-protein ligase
F: Angiomotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,50212
Polymers18,9336
Non-polymers5686
Water1,928107
1
A: E3 ubiquitin-protein ligase
B: Angiomotin


Theoretical massNumber of molelcules
Total (without water)6,3112
Polymers6,3112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-5 kcal/mol
Surface area3540 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase
D: Angiomotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4033
Polymers6,3112
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-4 kcal/mol
Surface area3530 Å2
MethodPISA
3
E: E3 ubiquitin-protein ligase
F: Angiomotin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7887
Polymers6,3112
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-53 kcal/mol
Surface area4500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.598, 91.598, 37.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein/peptide E3 ubiquitin-protein ligase


Mass: 4535.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD4L
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A6Q8PG51, HECT-type E3 ubiquitin transferase
#2: Protein/peptide Angiomotin


Mass: 1776.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q4VCS5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.0M Ammonium Sulfate, 0.1M BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9753 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9753 Å / Relative weight: 1
ReflectionResolution: 1.72→37.99 Å / Num. obs: 13684 / % possible obs: 99.94 % / Redundancy: 2 % / Biso Wilson estimate: 24.86 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0234 / Rrim(I) all: 0.331 / Net I/σ(I): 20.61
Reflection shellResolution: 1.72→1.781 Å / Redundancy: 2 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 1731 / CC1/2: 0.449 / Rrim(I) all: 0.0331 / % possible all: 95.77

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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: 1.88→37.98 Å / SU ML: 0.1887 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5278
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2279 1369 10.01 %
Rwork0.1854 12312 -
obs0.1896 13681 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.71 Å2
Refinement stepCycle: LAST / Resolution: 1.88→37.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 32 107 1307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811237
X-RAY DIFFRACTIONf_angle_d0.95821677
X-RAY DIFFRACTIONf_chiral_restr0.0535150
X-RAY DIFFRACTIONf_plane_restr0.007218
X-RAY DIFFRACTIONf_dihedral_angle_d6.5137166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.950.25611350.23441209X-RAY DIFFRACTION100
1.95-2.030.24251330.19711201X-RAY DIFFRACTION100
2.03-2.120.22341340.18931207X-RAY DIFFRACTION100
2.12-2.230.25261340.19561201X-RAY DIFFRACTION100
2.23-2.370.24621350.18361219X-RAY DIFFRACTION100
2.37-2.550.24451340.19411212X-RAY DIFFRACTION100
2.55-2.810.25791360.1931216X-RAY DIFFRACTION100
2.81-3.210.22541390.18921247X-RAY DIFFRACTION100
3.22-4.050.21151380.15881251X-RAY DIFFRACTION99.93
4.05-37.980.21071510.18821349X-RAY DIFFRACTION99.8
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)
13.488115310733.980236689450.3763313345489.412231739754.843533547444.042037493250.283604288402-0.705694565495-0.5065955835820.864696686627-0.425377175375-0.1203485563260.938049870205-0.1945446130120.04544146503640.227120469902-0.068607379731-0.007882331929030.2760463063250.06325664104580.2238114532064.8099313414-35.63662671245.70498329885
21.64793989350.4360743572990.9145008513166.900587957094.865579032325.997140598360.0330413380497-0.06328173242440.0754769826715-0.16281488402-0.0458980328909-0.130441085536-0.3080930339490.115757868837-0.02057499144680.112704107095-0.03471549630060.0272769718240.1343992076330.03476499222080.09467088413015.70307619695-25.67996539710.813854118458
32.67322601646-0.2946613637982.285893858889.45009074324-3.15984446765.98352778596-0.0433986604162-0.585678835755-0.1879877397110.7600282223410.3277187094060.74361472610.0034896663365-0.53406897362-0.2392960517750.1627744918870.02438634524050.05530952856990.2683262616850.04253401681620.134241673471-1.38957182027-28.55390054286.22133134746
46.73606725104-3.55550336656-8.569160029048.891876047789.419121846262.002011530840.6645575294291.6343666884-0.102134257588-1.24715225129-0.9666558255670.0554163093697-0.995564604657-0.732577086759-0.02433162977210.3394681954760.03828813030840.0573212511010.2804602598060.04035685530150.1814478669472.72234038807-19.08852278-3.99677090606
54.85979931375-5.28439888108-4.85865064558.384956375044.2209238445.294449547060.3360438957611.706839850160.0907379335661-0.709747809737-0.2790467413590.0470157240258-0.699492731548-0.2255178815890.01900614046320.284561912786-0.01239046789070.03131284562810.3358926121940.02408237872110.2185945674649.62754816062-28.5699913784-10.1381166881
68.16379935506-0.936075465141-0.4851098778845.944247791863.365983570313.282014878140.07685933115860.744379398640.188993915207-0.543123334053-0.00376261525638-0.217842702352-0.301761677257-0.10938217881-0.04603378646650.1511186703980.02089402748540.003733209896630.1804906547420.05538085526920.125928166467-10.3486009822-32.5693942869-7.15402217217
72.639175192660.395722855199-0.03141870194483.03010538117-0.4781384974626.058795181540.03441423258710.196819739770.735421322878-0.0315439909661-0.02183284870130.245888345908-0.5534938120890.06893407269230.07718678063230.166942592006-0.0142564156489-0.02023426980530.131774262670.04188389425280.295944509143-9.75115507019-27.0307018336-2.91939719549
83.09941691087-5.21903208892-4.193525914642.00726423385.764098441096.910458460080.2572525085240.5578651061970.229813567589-0.9917515630190.093842064899-0.611169233322-0.423721008096-0.166671994568-0.4377277408290.231516819458-0.0237736432636-0.01512429469250.1995368122680.004088846762310.265166555716-2.79498984492-28.8451899097-9.33311147907
94.548585108976.5309226325-4.32532002659.2611122576-6.188827134274.11924817220.530781952145-0.4657368288290.4849749692440.816161695139-0.3453539402110.380562307333-0.9697786617840.250400533034-0.2383193268790.3133176532130.006190589923130.003987843006780.22984344184-0.03811737969820.265937426459-11.2402840793-25.82485434293.23049457962
102.57786448181-2.222999190352.324801814498.67535586849-6.3152913638.24973663353-0.141016328653-0.00674619213436-0.1020653563320.364211088254-0.152931708772-0.271691452033-0.377335381231-0.1072185415630.3199423350470.227439787579-0.02740268645020.06646259032030.196738797523-0.008450022425190.15295649314210.0204632307-19.625527469624.0252955981
110.621104128299-1.39992678091-0.2777375351423.233972999130.2105082814022.55836755909-0.43573258381-0.4598809442871.05731711358-0.1561393980160.03420804174470.636827617117-0.290465972238-1.372001758750.3121234243030.3397260387750.152034116440.003940267391790.506595409118-0.06320408047610.473228268922-5.13526536032-11.807984931214.4517296446
129.15519855053-0.2791157882981.034476199044.390349674671.879447717384.154094559390.00826189530426-0.441428600648-0.06278468791440.2480049194760.0143304817678-0.146010231390.390110585179-0.1079536956760.004877310083260.205102897094-0.02194804334980.03110257341450.1374713681410.01512942341660.09651870715957.24827204721-19.094272730514.9461310157
139.513402020742.034399913315.979878445186.096495573463.247939171179.15612872352-0.262036500878-0.01722007301290.319310939119-0.300645569494-0.03083386225320.1806404363820.0959326643852-0.1387828615550.2776324962290.2630878917440.05264299588790.03141528455560.141759144353-0.01456231262550.1724024621263.79785255206-14.34597189759.61134842756
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 386 through 390 )AA386 - 3901 - 5
22chain 'A' and (resid 391 through 412 )AA391 - 4126 - 27
33chain 'A' and (resid 413 through 418 )AA413 - 41828 - 33
44chain 'B' and (resid 237 through 241 )BB237 - 2411 - 5
55chain 'B' and (resid 242 through 247 )BB242 - 2476 - 11
66chain 'C' and (resid 386 through 395 )CC386 - 3951 - 10
77chain 'C' and (resid 396 through 412 )CC396 - 41211 - 27
88chain 'C' and (resid 413 through 418 )CC413 - 41828 - 33
99chain 'D' and (resid 236 through 247 )DD236 - 2471 - 12
1010chain 'E' and (resid -4 through 395 )EE-4 - 3951 - 15
1111chain 'E' and (resid 396 through 400 )EE396 - 40016 - 20
1212chain 'E' and (resid 401 through 417 )EE401 - 41721 - 37
1313chain 'F' and (resid 233 through 247 )FF233 - 2471 - 15

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