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- PDB-43jx: NMR Solution Structure of the Monomeric Catalytic C-terminal Lobe... -

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Basic information

Entry
Database: PDB / ID: 43jx
TitleNMR Solution Structure of the Monomeric Catalytic C-terminal Lobe of the HECW2 HECT E3 Ubiquitin Ligase
ComponentsE3 ubiquitin-protein ligase HECW2
KeywordsLIGASE / HECW2 / HECT / HECT Ligase / C-Lobe
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / regulation of mitotic metaphase/anaphase transition / regulation of dendrite morphogenesis / mitotic spindle / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase HECW1/2, N-terminal / E3 ubiquitin-protein ligase HECW, C2 domain / E3 ubiquitin-protein ligase HECW1, helical box domain / N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2 / Helical box domain of E3 ubiquitin-protein ligase HECW1 / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. ...E3 ubiquitin-protein ligase HECW1/2, N-terminal / E3 ubiquitin-protein ligase HECW, C2 domain / E3 ubiquitin-protein ligase HECW1, helical box domain / N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2 / Helical box domain of E3 ubiquitin-protein ligase HECW1 / : / 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 HECW2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsDag, C. / Lambert, M. / Lee, W. / Tonelli, M. / Kazar, A.E.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government224N146 Turkey
CitationJournal: To Be Published
Title: NMR Solution Structure of the Monomeric Catalytic C-terminal Lobe of the HECW2 HECT E3 Ubiquitin Ligase
Authors: Dag, C. / Lambert, M. / Lee, W. / Tonelli, M. / Kazar, A.E.
History
DepositionJul 4, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase HECW2


Theoretical massNumber of molelcules
Total (without water)14,1221
Polymers14,1221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase HECW2 / HECT / C2 and WW domain-containing protein 2 / HECT-type E3 ubiquitin transferase HECW2 / NEDD4- ...HECT / C2 and WW domain-containing protein 2 / HECT-type E3 ubiquitin transferase HECW2 / NEDD4-like E3 ubiquitin-protein ligase 2


Mass: 14121.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HECW2, KIAA1301, NEDL2 / Plasmid: pET28b
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): Laq Iq
References: UniProt: Q9P2P5, HECT-type E3 ubiquitin transferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic33D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic4C(CO)NH TOCSY
151isotropic4H(CCO)NH-TOCSY
1151isotropic12D 1H-13C HSQC aliphatic
171isotropic13D 1H-13C NOESY aliphatic
1101isotropic13D 1H-15N NOESY
191isotropic3TRACT
181isotropic12D 1H-13C HSQC aromatic
161isotropic13D 1H-13C NOESY aromatic
1131isotropic12D CBHD
1121isotropic12D CBHDHE
1111isotropic33D HNCO
1161isotropic3HN(CA)CO

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM DTT, 0.15 mM DSS, 95% H2O/5% D2O
Label: 13C_15N_HECW2_C / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
5 mMDTTnatural abundance1
0.15 mMDSSnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 6 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails (eV)
Bruker AVANCE NEOBrukerAVANCE NEO11002Lakenvelder
Bruker AVANCE IIIBrukerAVANCE III9001Fleckvieh
Bruker AVANCE IIIBrukerAVANCE III7503Telemark
Bruker AVANCE IIIBrukerAVANCE III6004Kurgan

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Processing

NMR software
NameDeveloperClassification
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leechemical shift assignment
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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