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- PDB-5lg0: Solution NMR structure of Tryptophan to Alanine mutant of Arkadia... -

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Basic information

Entry
Database: PDB / ID: 5lg0
TitleSolution NMR structure of Tryptophan to Alanine mutant of Arkadia RING domain.
ComponentsE3 ubiquitin-protein ligase Arkadia
KeywordsLIGASE / Arkadia / Rnf111 / E3 Ubiquitin ligase / RING domain / Tryptophan / TGF-b / UbcH5b E2 enzyme
Function / homology
Function and homology information


SUMO polymer binding / global genome nucleotide-excision repair / pattern specification process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of protein ubiquitination / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RING-type E3 ubiquitin transferase / PML body ...SUMO polymer binding / global genome nucleotide-excision repair / pattern specification process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of protein ubiquitination / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RING-type E3 ubiquitin transferase / PML body / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase Arkadia, N-terminal / E3 ubiquitin-protein ligase Arkadia N-terminus / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Arkadia
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular mechanics
AuthorsBirkou, M. / Chasapis, C.T. / Loutsidou, A.K. / Bentrop, D. / Lelli, M. / Herrmann, T. / Episkopou, V. / Spyroulias, G.A.
Funding support Greece, 1items
OrganizationGrant numberCountry
FP7-CAPACITIES - Research Potentials REGPOT "SEE-DRUG"285950 Greece
CitationJournal: J. Mol. Biol. / Year: 2017
Title: A Residue Specific Insight into the Arkadia E3 Ubiquitin Ligase Activity and Conformational Plasticity.
Authors: Birkou, M. / Chasapis, C.T. / Marousis, K.D. / Loutsidou, A.K. / Bentrop, D. / Lelli, M. / Herrmann, T. / Carthy, J.M. / Episkopou, V. / Spyroulias, G.A.
History
DepositionJul 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / database_2 / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.database_code / _pdbx_database_related.db_id
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Arkadia
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9763
Polymers7,8451
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6180 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 31target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein E3 ubiquitin-protein ligase Arkadia / RING finger protein 111


Mass: 7844.902 Da / Num. of mol.: 1 / Mutation: W972A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF111 / Plasmid: pGex-47-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6ZNA4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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
151isotropic23D 1H-15N NOESY
1161isotropic23D HNHA
122isotropic23D HN(CA)CB
132isotropic23D CBCA(CO)NH
142isotropic23D HNCA
162isotropic23D 1H-13C NOESY aliphatic
172isotropic23D 1H-13C NOESY aromatic
182isotropic23D (H)CCH-TOCSY
1142isotropic22D 1H-13C HSQC
192isotropic13D HN(CA)CB
1132isotropic13D CBCA(CO)NH
1122isotropic13D 1H-13C NOESY aliphatic
1112isotropic13D 1H-13C NOESY aromatic
1101isotropic13D 1H-15N NOESY
1151isotropic12D 1H-15N HSQC
1172isotropic14D APSY-HACANH
1182isotropic15D APSY-CBCA(CO)NH
1192isotropic15D APSY-(HA)CA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-99% 15N] ARKADIA RING W972A, 50 mM potassium phosphate, 2 mM DSS, 90% H2O/10% D2O15N-Sample90% H2O/10% D2O
solution20.6 mM [U-99% 13C; U-99% 15N] ARKADIA RING W972A, 50 mM potassium phosphate, 2 mM DSS, 90% H2O/10% D2O13C/15N-Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMARKADIA RING W972A[U-99% 15N]1
50 mMpotassium phosphatenatural abundance1
2 mMDSSnatural abundance1
0.6 mMARKADIA RING W972A[U-99% 13C; U-99% 15N]2
50 mMpotassium phosphatenatural abundance2
2 mMDSSnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: Conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker SB AvanceIIIBrukerSB AvanceIII10001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4Keller and Wuthrichchemical shift assignment
UNIO10Torsten Herrmannchemical shift assignment
UNIO10Torsten Herrmannstructure calculation
Amber5Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular mechanics / Software ordinal: 4
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 31 / Conformers submitted total number: 31

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