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- PDB-5tjq: Structure of WWP2 2,3-linker-HECT -

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Basic information

Entry
Database: PDB / ID: 5tjq
TitleStructure of WWP2 2,3-linker-HECT
ComponentsNEDD4-like E3 ubiquitin-protein ligase WWP2,NEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsTRANSFERASE / WWP2 / HECT Domain / WW2 / WWP1 / ITCH / autoinhibition
Function / homology
Function and homology information


negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle ...negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / protein K63-linked ubiquitination / negative regulation of Notch signaling pathway / ubiquitin ligase complex / protein autoubiquitination / regulation of membrane potential / negative regulation of DNA-binding transcription factor activity / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 / nucleus / membrane / 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. ...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: 2.75 Å
AuthorsChen, Z. / Gabelli, S.B.
CitationJournal: Mol. Cell / Year: 2017
Title: A Tunable Brake for HECT Ubiquitin Ligases.
Authors: Chen, Z. / Jiang, H. / Xu, W. / Li, X. / Dempsey, D.R. / Zhang, X. / Devreotes, P. / Wolberger, C. / Amzel, L.M. / Gabelli, S.B. / Cole, P.A.
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP2,NEDD4-like E3 ubiquitin-protein ligase WWP2


Theoretical massNumber of molelcules
Total (without water)53,4421
Polymers53,4421
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.041, 62.581, 102.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NEDD4-like E3 ubiquitin-protein ligase WWP2,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(DE3) codon plus
References: UniProt: O00308, HECT-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.76 % / Mosaicity: 0.629 ° / Mosaicity esd: 0.005 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 0.1 M MMT (DL-malic acid, MES, Tris-base in molar ratio of 1:2:2) pH 6.0, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 10662 / % possible obs: 99.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.029 / Rrim(I) all: 0.071 / Χ2: 0.896 / Net I/σ(I): 8.9 / Num. measured all: 63592
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.85.20.4635040.8340.2160.5130.4798.6
2.8-2.855.30.4215370.9050.1990.4680.48199.3
2.85-2.95.70.4045200.9080.1840.4450.49999.8
2.9-2.965.70.3545050.9380.1610.390.532100
2.96-3.036.30.2715310.9690.1160.2960.509100
3.03-3.16.50.2395280.9820.10.2590.515100
3.1-3.176.40.2135240.980.0910.2320.56199.8
3.17-3.266.40.1765330.9830.0740.1910.60599.8
3.26-3.366.20.1385390.9930.060.1510.642100
3.36-3.4660.1115190.9940.050.1220.68999.4
3.46-3.5960.1085270.9930.0480.1190.77799.8
3.59-3.7360.0875340.9960.0380.0950.9199.8
3.73-3.96.30.0735420.9960.0310.0790.911100
3.9-4.116.20.0595370.9980.0260.0650.97999.8
4.11-4.366.10.0555350.9980.0250.0611.16799.3
4.36-4.75.70.0495300.9980.0220.0541.30498.3
4.7-5.175.90.0465470.9980.0210.0511.26198.4
5.17-5.926.10.0475430.9980.0210.0521.2998.9
5.92-7.465.70.0475610.9960.0220.0521.51298.8
7.46-505.40.0435660.9980.0210.0482.28492.8

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y07

4y07


Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.855 / WRfactor Rfree: 0.317 / WRfactor Rwork: 0.2249 / FOM work R set: 0.7514 / SU B: 20.166 / SU ML: 0.394 / SU Rfree: 0.4899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.49 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.317 483 4.6 %RANDOM
Rwork0.2249 ---
obs0.229 10094 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 206.26 Å2 / Biso mean: 87.323 Å2 / Biso min: 42.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2---5.01 Å20 Å2
3---5.73 Å2
Refinement stepCycle: final / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 11 3056
Biso mean---63.08 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193142
X-RAY DIFFRACTIONr_bond_other_d0.0030.022954
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9514235
X-RAY DIFFRACTIONr_angle_other_deg1.03736793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51923.494166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93815573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6451524
X-RAY DIFFRACTIONr_chiral_restr0.080.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02790
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 24 -
Rwork0.325 726 -
all-750 -
obs--99.21 %

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