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- PDB-2yrg: Solution structure of the B-box domain from tripartite motif-cont... -

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Basic information

Entry
Database: PDB / ID: 2yrg
TitleSolution structure of the B-box domain from tripartite motif-containing protein 5
ComponentsTripartite motif-containing protein 5
KeywordsLIGASE / B-box domain / Tripartite motif-containing protein 5 / RING finger protein 88 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / pattern recognition receptor activity / protein K63-linked ubiquitination / positive regulation of autophagy / activation of innate immune response / positive regulation of DNA-binding transcription factor activity / P-body ...regulation of viral entry into host cell / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / negative regulation of viral entry into host cell / pattern recognition receptor activity / protein K63-linked ubiquitination / positive regulation of autophagy / activation of innate immune response / positive regulation of DNA-binding transcription factor activity / P-body / RING-type E3 ubiquitin transferase / autophagy / protein polyubiquitination / ubiquitin-protein transferase activity / Interferon gamma signaling / ubiquitin protein ligase activity / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / transcription coactivator activity / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / : / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain ...Zinc finger, RING-type, eukaryotic / : / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsQin, X.R. / Hayahsi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the B-box domain from tripartite motif-containing protein 5
Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE There is a conflict 130 LEU to PRO in ref.2 BAB55218

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4783
Polymers6,3471
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tripartite motif-containing protein 5 / RING finger protein 88


Mass: 6346.976 Da / Num. of mol.: 1 / Fragment: B-box domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: TRIM5 / Plasmid: P070115-01
References: UniProt: Q9C035, 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
NMR detailsText: spectrometer_id 1 for 3D_15N_separated_NOESY, spectrometer_id 2 for 3D_13C_separated_NOESY;

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Sample preparation

DetailsContents: 1.13mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2, 1mM IDA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20030801Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.982Kobayashi, 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: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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