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- PDB-9eqh: WWP2 WW2-2,3-linker-HECT (WWP2-LH) -

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Basic information

Entry
Database: PDB / ID: 9eqh
TitleWWP2 WW2-2,3-linker-HECT (WWP2-LH)
ComponentsIsoform 2 of NEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsLIGASE / Ubiquitin
Function / homology
Function and homology information


negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination ...negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / negative regulation of transporter activity / regulation of monoatomic ion transmembrane transport / negative regulation of Notch signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / protein K63-linked ubiquitination / RHOU GTPase cycle / transcription factor binding / protein autoubiquitination / ubiquitin ligase complex / regulation of membrane potential / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / negative regulation of DNA-binding transcription factor activity / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein ubiquitination / symbiont entry into host cell / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / membrane / nucleus / 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 / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain ...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) / 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
NEDD4-like E3 ubiquitin-protein ligase WWP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsDudey, A.P. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
BigC Cancer CharityResearch Grant 19-14R United Kingdom
CitationJournal: To Be Published
Title: Expanding the Inhibitor Space of the WWP1 and WWP2 HECT E3 Ligases
Authors: Dudey, A.P. / Rigby, J.M. / Hughes, G.R. / Stephenson, G.R. / Storr, T.E. / Chantry, A. / Hemmings, A.M.
History
DepositionMar 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of NEDD4-like E3 ubiquitin-protein ligase WWP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6494
Polymers53,4421
Non-polymers2073
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.009, 90.27, 111.177
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Isoform 2 of NEDD4-like E3 ubiquitin-protein ligase WWP2 / Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain- ...Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain-containing protein 2


Mass: 53441.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP2 / Plasmid: pGEX6p-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus RP
References: UniProt: O00308, HECT-type E3 ubiquitin transferase
#2: 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: Square Plates
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MMT pH 6.0, 25 % PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.046→70.079 Å / Num. obs: 28618 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.075 / Rrim(I) all: 0.205 / Net I/σ(I): 6.9
Reflection shellResolution: 2.046→5.552 Å / Num. unique obs: 1419 / CC1/2: 0.486 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→70.079 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.866 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2749 1357 4.783 %
Rwork0.2134 27012 -
all0.216 --
obs-28369 99.272 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.688 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å2-0 Å20 Å2
2--3.221 Å2-0 Å2
3----0.781 Å2
Refinement stepCycle: LAST / Resolution: 2.05→70.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 13 105 3636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123630
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163315
X-RAY DIFFRACTIONr_angle_refined_deg2.2221.8444899
X-RAY DIFFRACTIONr_angle_other_deg1.0111.7687635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9455423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.95526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12810636
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.62210194
X-RAY DIFFRACTIONr_chiral_restr0.1230.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024334
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02930
X-RAY DIFFRACTIONr_nbd_refined0.1860.2764
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1370.23159
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21746
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.21906
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2144
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.216
X-RAY DIFFRACTIONr_nbd_other0.1180.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0570.25
X-RAY DIFFRACTIONr_mcbond_it6.3994.9161692
X-RAY DIFFRACTIONr_mcbond_other6.3964.9161692
X-RAY DIFFRACTIONr_mcangle_it8.7758.8632115
X-RAY DIFFRACTIONr_mcangle_other8.7738.8652116
X-RAY DIFFRACTIONr_scbond_it6.7855.4231938
X-RAY DIFFRACTIONr_scbond_other6.7845.4241939
X-RAY DIFFRACTIONr_scangle_it10.0539.7372784
X-RAY DIFFRACTIONr_scangle_other10.0529.7372785
X-RAY DIFFRACTIONr_lrange_it13.06749.7084170
X-RAY DIFFRACTIONr_lrange_other13.08349.7544156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.05-2.1030.3311160.3419360.33920950.9010.88897.94750.329
2.103-2.1610.314940.33518660.33419810.8870.89198.93990.322
2.161-2.2230.346940.30418720.30619760.9120.91999.49390.285
2.223-2.2920.333860.2818190.28319090.9210.93199.79050.258
2.292-2.3670.298790.27117700.27218500.9080.9499.94590.245
2.367-2.450.333850.27117360.27418280.9250.94199.61710.247
2.45-2.5420.31940.23616330.2417300.9440.95899.82660.209
2.542-2.6460.289770.22115770.22516580.950.96499.75870.198
2.646-2.7630.255720.20715600.2116340.9560.9799.87760.182
2.763-2.8980.32700.22114640.22615340.9360.9651000.198
2.898-3.0540.338670.2214130.22514800.9320.9661000.201
3.054-3.2390.232620.21513400.21614020.9640.9691000.199
3.239-3.4620.303780.21212360.21713140.9320.9681000.203
3.462-3.7390.265640.19311690.19612410.9520.97599.35540.19
3.739-4.0950.247540.18410720.18711390.9550.97798.85870.186
4.095-4.5760.231350.169880.16210400.970.98398.36540.171
4.576-5.280.197340.1568820.1579340.980.98598.07280.169
5.28-6.4580.255400.1817370.1857950.9620.98297.73590.194
6.458-9.0940.265350.1865840.1916370.960.97997.17430.209
9.094-70.0790.232210.2063470.2083880.9650.97694.84540.252

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