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- PDB-8enp: UBE3A isoform 3 AZUL -

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Basic information

Entry
Database: PDB / ID: 8enp
TitleUBE3A isoform 3 AZUL
ComponentsIsoform III of Ubiquitin-protein ligase E3A
KeywordsLIGASE / ubiquitin ligase / proteasome interaction
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / androgen receptor signaling pathway / locomotory exploration behavior / progesterone receptor signaling pathway ...sperm entry / positive regulation of Golgi lumen acidification / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / androgen receptor signaling pathway / locomotory exploration behavior / progesterone receptor signaling pathway / protein autoubiquitination / protein K48-linked ubiquitination / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / proteasome complex / response to cocaine / positive regulation of protein ubiquitination / response to progesterone / regulation of synaptic plasticity / brain development / response to hydrogen peroxide / regulation of circadian rhythm / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / 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 / metal 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 / simulated annealing
AuthorsBregnard, T.A. / Bezsonova, I.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128864 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI135451 United States
National Science Foundation (NSF, United States)NSF 1616184 United States
CitationJournal: To Be Published
Title: Differences in structure, dynamics and Zn-coordination between isoforms of human ubiquitin ligase UBE3A
Authors: Bregnard, T.A. / Fairchild, D. / Chen, X. / Erlandsen, H. / Walters, K.J. / Korzhnev, D.M. / Bezsonova, I.
History
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform III of Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6962
Polymers9,6311
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, structural zinc is required for proper folding
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform III of 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: 9630.942 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Plasmid: pET28b+ / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CO)CA
151isotropic13D HN(CA)CB
161isotropic13D CBCA(CO)NH
171isotropic13D HBHA(CO)NH
181isotropic12D 1H-13C HSQC
191isotropic13D CCH-TOCSY
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 1.7 mM [U-99% 13C; U-99% 15N] UBE3A iso 3 AZUL, 10 mM MOPS, 450 mM sodium chloride, 10 mM beta-mercaptoethanol, 10 uM zinc sulfate, 90% H2O/10% D2O
Label: UBE3A AZUL iso3 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mMUBE3A iso 3 AZUL[U-99% 13C; U-99% 15N]1
10 mMMOPSnatural abundance1
450 mMsodium chloridenatural abundance1
10 mMbeta-mercaptoethanolnatural abundance1
10 uMzinc sulfatenatural abundance1
Sample conditionsIonic strength: 450 mM / Label: structure conditions / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRFAM-SPARKYLee, Tonelli, and Markleychemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: CNS refinement in explicit water
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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