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- PDB-9vg5: NMR Solution Structure of the Monomeric Catalytic C-terminal Lobe... -

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Basic information

Entry
Database: PDB / ID: 9vg5
TitleNMR Solution Structure of the Monomeric Catalytic C-terminal Lobe of the E6AP HECT E3 Ubiquitin Ligase
ComponentsUbiquitin-protein ligase E3A
KeywordsLIGASE / HECT ligase / E6AP / E3 ligase / C-lobe
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / locomotory exploration behavior / androgen receptor signaling pathway / postsynaptic cytosol ...sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / locomotory exploration behavior / androgen receptor signaling pathway / postsynaptic cytosol / protein K48-linked ubiquitination / progesterone receptor signaling pathway / protein autoubiquitination / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / proteasome complex / response to progesterone / positive regulation of protein ubiquitination / response to cocaine / regulation of circadian rhythm / brain development / regulation of synaptic plasticity / response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / synaptic vesicle / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with
Similarity search - Domain/homology
Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDag, C. / Lambert, M. / Lohr, F. / Lee, W. / Kazar, A.E. / Dotsch, V.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other governmentTUBITAK 122Z747 Turkey
CitationJournal: To Be Published
Title: NMR Solution Structure of the Monomeric Catalytic C-terminal Lobe of the E6AP HECT E3 Ubiquitin Ligase
Authors: Dag, C. / Lambert, M. / Lohr, F. / Lee, W. / Kazar, A.E. / Dotsch, V.
History
DepositionJun 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-protein ligase E3A


Theoretical massNumber of molelcules
Total (without water)13,1741
Polymers13,1741
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 Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6-associated protein / Oncogenic protein-associated protein E6-AP / Renal carcinoma antigen NY-REN-54


Mass: 13174.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta 2
References: UniProt: Q05086, 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
111isotropic32D 1H-15N HSQC
121isotropic13D HNCO
131isotropic23D HN(CA)CO
141isotropic43D HN(CA)CB
151isotropic23D HN(COCA)CB
161isotropic13D 1H-13C NOESY aliphatic
171isotropic53D 1H-13C NOESY aromatic
181isotropic13D 1H-15N NOESY
191isotropic43D H(CCO)NH
1101isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 20 mM NaPi, 100 mM NaCl, 0.15 mM DSS, 5 mM DTT, 95% H2O/5% D2O
Details: 0.4mM e6AP C lobe 20mM NaPi pH7.7, 100mM NaCl, 5% D2O 0.15mM DSS, 5mM DTT
Label: 13C_15N_E6AP_HECT C-lobe / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMNaPinatural abundance1
100 mMNaClnatural abundance1
0.15 mMDSSnatural abundance1
5 mMDTTnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: 13C_15N_E6AP_HECT C-lobe / pH: 7.7 / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO12003
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE NEOBrukerAVANCE NEO9002
Bruker AVANCE IIIBrukerAVANCE III8004
Bruker AVANCE IIIBrukerAVANCE III7005

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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
Pokypeak picking
RefinementMethod: torsion angle dynamics / 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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