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- PDB-2d8u: Solution structure of the B-box domain of the human tripartite mo... -

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Basic information

Entry
Database: PDB / ID: 2d8u
TitleSolution structure of the B-box domain of the human tripartite motif-containing 63 protein
ComponentsUbiquitin ligase TRIM63
KeywordsLIGASE / tripartite motif-containing 63 / TRIM63 / Muscle-specific RING finger protein 1 / MuRF1 / RING finger protein 28 / Striated muscle RING zinc finger protein / Iris ring finger protein / zf-B_box / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / negative regulation of cardiac muscle hypertrophy / M band / negative regulation of glycolytic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucocorticoid / titin binding / muscle contraction / response to interleukin-1 ...response to electrical stimulus involved in regulation of muscle adaptation / skeletal muscle atrophy / negative regulation of cardiac muscle hypertrophy / M band / negative regulation of glycolytic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucocorticoid / titin binding / muscle contraction / response to interleukin-1 / RING-type E3 ubiquitin transferase / Z disc / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / microtubule / protein ubiquitination / signal transduction / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase TRIM63, RING finger, HC subclass / COS domain / COS domain profile. / Zinc finger, RING-type, eukaryotic / : / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. ...E3 ubiquitin-protein ligase TRIM63, RING finger, HC subclass / COS domain / COS domain profile. / Zinc finger, RING-type, eukaryotic / : / RING-type zinc-finger / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Classic Zinc Finger / Double Stranded RNA Binding Domain / 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 TRIM63
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K. / Kigawa, T. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the B-box domain of the human tripartite motif-containing 63 protein
Authors: Miyamoto, K. / Kigawa, T. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionDec 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2006Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin ligase TRIM63
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9163
Polymers6,7851
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 Ubiquitin ligase TRIM63 / Tripartite motif-containing 63 / Muscle-specific RING finger protein 1 / MuRF1 / MURF-1 / RING ...Tripartite motif-containing 63 / Muscle-specific RING finger protein 1 / MuRF1 / MURF-1 / RING finger protein 28 / Striated muscle RING zinc finger protein / Iris RING finger protein


Mass: 6784.683 Da / Num. of mol.: 1 / Fragment: zf-B box
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TRIM63 / Plasmid: P050302-45
References: UniProt: Q969Q1, 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: 2.09mM zf-B_box U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZNCl2; 1.0mM IDA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 296 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
KUJIRA0.9321Kobayashi, 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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