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- PDB-2ecw: Solution structure of the Zinc finger, C3HC4 type (RING finger) d... -

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Entry
Database: PDB / ID: 2ecw
TitleSolution structure of the Zinc finger, C3HC4 type (RING finger) domain Tripartite motif protein 30
ComponentsTripartite motif-containing protein 30
KeywordsAPOPTOSIS / Metal Binding Protein / 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 / negative regulation of toll-like receptor signaling pathway / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / positive regulation of autophagy / response to bacterium / autophagy ...regulation of viral entry into host cell / negative regulation of toll-like receptor signaling pathway / negative regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / positive regulation of autophagy / response to bacterium / autophagy / protein polyubiquitination / positive regulation of protein catabolic process / regulation of protein localization / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / regulation of gene expression / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / positive regulation of viral entry into host cell / protein ubiquitination / innate immune response / protein kinase binding / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Tripartite motif-containing protein 5 / 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. / Zinc finger, C3HC4 type (RING finger) / SPRY domain ...Tripartite motif-containing protein 5 / 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. / Zinc finger, C3HC4 type (RING finger) / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / 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 / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tripartite motif-containing protein 30A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAbe, H. / Miyamoto, K. / Tochio, N. / Yoneyama, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Zinc finger, C3HC4 type (RING finger) domain Tripartite motif protein 30
Authors: Abe, H. / Miyamoto, K. / Tochio, N. / Yoneyama, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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: Tripartite motif-containing protein 30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3003
Polymers9,1691
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-containing protein 30 / Down regulatory protein of interleukin 2 receptor


Mass: 9169.468 Da / Num. of mol.: 1 / Fragment: RING-type, residues 6-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Trim30 / Plasmid: P060417-23 / References: UniProt: P15533
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE RESIDUE IS LYS BASED ON REFERENCE 4 IN THE DATABASE, TRI30_MOUSE.

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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: 1.13mM Protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 50uM Zncl2+1mM IDA; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMNMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9747Kobayashi, 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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