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- PDB-2eqg: Solution structure of the first A20-type zinc finger domain from ... -

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Basic information

Entry
Database: PDB / ID: 2eqg
TitleSolution structure of the first A20-type zinc finger domain from human tumor necrosis factor, alpha-induced protein3
ComponentsTumor necrosis factor, alpha-induced protein 3
KeywordsHYDROLASE / zf-A20 domain / Tumor necrosis factor / alpha-induced protein 3 / Putative DNA-binding protein A20 / Zinc finger protein A20 / 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 vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / protein K33-linked deubiquitination / protein K29-linked deubiquitination ...regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of B cell activation / negative regulation of chronic inflammatory response / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / regulation of germinal center formation / B-1 B cell homeostasis / regulation of defense response to virus by host / protein K48-linked deubiquitination / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of hepatocyte proliferation / protein K63-linked deubiquitination / negative regulation of bone resorption / TNFR1-induced proapoptotic signaling / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / K63-linked polyubiquitin modification-dependent protein binding / response to muramyl dipeptide / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein deubiquitination / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoskeleton organization / negative regulation of protein ubiquitination / negative regulation of innate immune response / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / response to molecule of bacterial origin / NOD1/2 Signaling Pathway / kinase binding / negative regulation of inflammatory response / cellular response to hydrogen peroxide / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Ovarian tumor domain proteases / cell migration / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / DNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CD2-Gal4 - #30 / CD2-Gal4 / : / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile. ...CD2-Gal4 - #30 / CD2-Gal4 / : / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZhang, H.P. / Hayahsi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution structure of the first A20-type zinc finger domain from human tumor necrosis factor, alpha-induced protein3
Authors: Zhang, H.P. / Hayashi, F. / Yokoyama, S.
History
DepositionMar 30, 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 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor, alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2782
Polymers5,2131
Non-polymers651
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/peptide Tumor necrosis factor, alpha-induced protein 3 / Putative DNA-binding protein A20 / Zinc finger protein A20


Mass: 5212.726 Da / Num. of mol.: 1 / Fragment: A20-type zinc finger domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: TNFAIP3 / Plasmid: P070115-04 / References: UniProt: P21580, Hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.08mM 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: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9818Kobayashi, 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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