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- PDB-2ct2: Solution Structure of the RING domain of the Tripartite motif pro... -

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Basic information

Entry
Database: PDB / ID: 2ct2
TitleSolution Structure of the RING domain of the Tripartite motif protein 32
ComponentsTripartite motif protein 32
KeywordsLIGASE / Tripartite motif protein 32 / Zinc-finger protein HT2A / Tat-interacting protein / RING domain / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


actin ubiquitination / positive regulation of interleukin-17-mediated signaling pathway / positive regulation of chemokine (C-C motif) ligand 20 production / striated muscle myosin thick filament / positive regulation of striated muscle cell differentiation / suppression of viral release by host / free ubiquitin chain polymerization / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of cilium assembly / positive regulation of autophagosome assembly ...actin ubiquitination / positive regulation of interleukin-17-mediated signaling pathway / positive regulation of chemokine (C-C motif) ligand 20 production / striated muscle myosin thick filament / positive regulation of striated muscle cell differentiation / suppression of viral release by host / free ubiquitin chain polymerization / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of cilium assembly / positive regulation of autophagosome assembly / negative regulation of viral transcription / tissue homeostasis / Tat protein binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of neurogenesis / muscle cell cellular homeostasis / positive regulation of cell motility / cellular response to stress / myosin binding / response to starvation / axon development / fat cell differentiation / positive regulation of proteolysis / response to tumor necrosis factor / autophagosome assembly / protein K63-linked ubiquitination / response to UV / negative regulation of fibroblast proliferation / positive regulation of cell cycle / translation initiation factor binding / positive regulation of autophagy / positive regulation of neuron differentiation / Regulation of innate immune responses to cytosolic DNA / cellular response to amino acid starvation / autophagosome / positive regulation of DNA-binding transcription factor activity / ubiquitin binding / RING-type E3 ubiquitin transferase / protein polyubiquitination / positive regulation of protein catabolic process / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of cell growth / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / protein ubiquitination / positive regulation of cell migration / innate immune response / centrosome / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like ...: / NHL repeat profile. / NHL repeat / NHL repeat / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM32
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K. / Tochio, N. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the RING domain of the Tripartite motif protein 32
Authors: Miyamoto, K. / Tochio, N. / Sato, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _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
Remark 650HELIX Determination method: author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tripartite motif protein 32
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6243
Polymers9,4931
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 / 100target function, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Tripartite motif protein 32 / Zinc-finger protein HT2A / 72 kDa Tat-interacting protein


Mass: 9492.962 Da / Num. of mol.: 1 / Fragment: RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TRIM32 / Plasmid: P041101-17
References: UniProt: Q13049, 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
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.47mM RING domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZNCl2; 0.1mM NTA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.925Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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