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- PDB-2m9y: Solution Structure of the Catalytic Domain of HHARI -

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Basic information

Entry
Database: PDB / ID: 2m9y
TitleSolution Structure of the Catalytic Domain of HHARI
ComponentsE3 ubiquitin-protein ligase ARIH1
KeywordsLIGASE / HHARI / RING2 / E3 ligase / Zn-binding
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 / Modulation of host responses by IFN-stimulated genes / RSV-host interactions / ubiquitin ligase complex / Cajal body / PKR-mediated signaling ...PKR/eIFalpha signaling / ubiquitin-like protein transferase activity / Lewy body / RBR-type E3 ubiquitin transferase / ubiquitin conjugating enzyme binding / Modulation of host responses by IFN-stimulated genes / RSV-host interactions / ubiquitin ligase complex / Cajal body / PKR-mediated signaling / ISG15 antiviral mechanism / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / nuclear body / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
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 / IBR domain / In Between Ring fingers / TRIAD supradomain ...: / 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 / 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 / simulated annealing, torsion angle dynamics
AuthorsMercier, P. / Spratt, D.E. / Shaw, G.S.
CitationJournal: Plos One / Year: 2013
Title: Structure of the HHARI catalytic domain shows glimpses of a HECT E3 ligase.
Authors: Spratt, D.E. / Mercier, P. / Shaw, G.S.
History
DepositionJun 24, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / 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: E3 ubiquitin-protein ligase ARIH1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5703
Polymers8,4391
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein E3 ubiquitin-protein ligase ARIH1 / H7-AP2 / HHARI / Monocyte protein 6 / MOP-6 / Protein ariadne-1 homolog / ARI-1 / UbcH7-binding ...H7-AP2 / HHARI / Monocyte protein 6 / MOP-6 / Protein ariadne-1 homolog / ARI-1 / UbcH7-binding protein / UbcM4-interacting protein / Ubiquitin-conjugating enzyme E2-binding protein 1


Mass: 8439.263 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (UNP residues 325-396) / Mutation: C357S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARIH1, ARI, MOP6, UBCH7BP, HUSSY-27 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: Q9Y4X5, 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-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1413D 1H-15N NOESY
1513D 1H-13C NOESY aliphatic
1623D 1H-13C NOESY aromatic
1713D HN(CA)CB
1813D CBCA(CO)NH
1923D 1H-13C NOESY aliphatic
11022D (HB)CB(CGCD)HD
11122D (HB)CB(CGCDCE)HE
11222D HCN

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES, 120 mM sodium chloride, 5 mM DTT, 2.3 mM [U-98% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
220 mM MES, 120 mM sodium chloride, 5 mM DTT, 2.3 mM [U-98% 13C; U-98% 15N] protein, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES-11
120 mMsodium chloride-21
5 mMDTT-31
2.3 mMentity_1-4[U-98% 15N]1
20 mMMES-52
120 mMsodium chloride-62
5 mMDTT-72
2.3 mMentity_1-8[U-98% 13C; U-98% 15N]2
Sample conditionsIonic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVarian VnmrJ 2.2DVariancollection
NMRPipe2013.021.23.09Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawVer 7.9 Rev 2013.021.23.09Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView9.0.0beta76Johnson, One Moon Scientificdata analysis
NMRView9.0.0beta76Johnson, One Moon Scientificchemical shift assignment
NMRView9.0.0beta76Johnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorerefinement
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: WITH EXPLICIT SOLVENT AND FULL ELECTROSTATICS, WITH EXPLICIT SOLVENT AND FULL ELECTROSTATICS
NMR constraintsNOE constraints total: 1321 / NOE intraresidue total count: 349 / NOE long range total count: 380 / NOE medium range total count: 179 / NOE sequential total count: 413
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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