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- PDB-1wd2: Solution Structure of the C-terminal RING from a RING-IBR-RING (T... -

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Basic information

Entry
Database: PDB / ID: 1wd2
TitleSolution Structure of the C-terminal RING from a RING-IBR-RING (TRIAD) motif
ComponentsAriadne-1 protein homolog
KeywordsLIGASE / RING / IBR / TRIAD / ZINC FINGER
Function / homology
Function and homology information


PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / Cajal body / ubiquitin ligase complex / PKR-mediated signaling / ISG15 antiviral mechanism / protein polyubiquitination ...PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / Cajal body / ubiquitin ligase complex / PKR-mediated signaling / ISG15 antiviral mechanism / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. ...: / E3 ubiquitin-protein ligase ARIH1, UBA-like domain / Ariadne domain / Ariadne domain / E3 ubiquitin ligase RBR family / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 ARIH1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, , simulated annealing
AuthorsCapili, A.D. / Edghill, E.L. / Wu, K. / Borden, K.L.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of the C-terminal RING Finger from a RING-IBR-RING/TRIAD Motif Reveals a Novel Zinc-binding Domain Distinct from a RING
Authors: Capili, A.D. / Edghill, E.L. / Wu, K. / Borden, K.L.B.
History
DepositionMay 11, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ariadne-1 protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0682
Polymers7,0031
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #6closest to the average

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Components

#1: Protein Ariadne-1 protein homolog / / ARI-1 / Ubiquitin-conjugating enzyme E2- binding protein 1 / UbcH7-binding protein / UbcM4- ...ARI-1 / Ubiquitin-conjugating enzyme E2- binding protein 1 / UbcH7-binding protein / UbcM4-interacting protein / HHARI / H7-AP2 / HUSSY-27 / MOP-6


Mass: 7002.953 Da / Num. of mol.: 1 / Fragment: C-terminal RING
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y4X5, ubiquitin-protein ligase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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-IDType
111HNCA & HN(CO)CA
121HN(CA)CB & HN(CO)CACB
131(H)C(CO)NH-TOCSY
141H(CCO)NH-TOCSY
1523D 15N-separated TOCSY
1623D 15N-separated NOESY
1723D 15N-separated TOCSY
182HNHA
1933D 13C-separated NOESY
11033D 13C-separated (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM RING2, U-15N,13C; 20mM Tris-d11(pH 8.0), 120mM NaCl90% H2O/10% D2O
21mM RING2, U-15N; 20mM Tris-d11(pH 8.0), 120mM NaCl90% H2O/10% D2O
31mM RING2, U-13C; 20mM Tris-d11(pH 8.0), 120mM NaCl100% D2O
Sample conditionsIonic strength: 120mM NaCl / pH: 8.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRView3.1.2Johnson, B.A., Blevins, R.data analysis
CNS1.1Brunger, A.T. et al.structure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics, , simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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