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

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Entry
Database: PDB / ID: 2ecy
TitleSolution structure of the Zinc finger, C3HC4 type (RING finger)" domain of TNF receptor-associated factor 3
ComponentsTNF receptor-associated factor 3
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 interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / serine/threonine protein kinase complex / CD40 receptor complex / TRIF-dependent toll-like receptor signaling pathway / regulation of defense response to virus / regulation of proteolysis / thioesterase binding ...regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / serine/threonine protein kinase complex / CD40 receptor complex / TRIF-dependent toll-like receptor signaling pathway / regulation of defense response to virus / regulation of proteolysis / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / negative regulation of NF-kappaB transcription factor activity / toll-like receptor signaling pathway / type I interferon-mediated signaling pathway / protein K63-linked ubiquitination / positive regulation of type I interferon production / ubiquitin ligase complex / tumor necrosis factor-mediated signaling pathway / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / regulation of cytokine production / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / protein phosphatase binding / regulation of apoptotic process / defense response to virus / endosome membrane / endosome / ubiquitin protein ligase binding / apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / TNF receptor-associated factor 2/3/5, RING domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain ...: / TNF receptor-associated factor 2/3/5, RING domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
TNF receptor-associated factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
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 of TNF receptor-associated factor 3
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: TNF receptor-associated factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2673
Polymers7,1361
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, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein TNF receptor-associated factor 3 / CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein ...CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein / LAP1 / CAP-1


Mass: 7136.255 Da / Num. of mol.: 1 / Fragment: RING-type, residues 8-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: TRAF3 / Plasmid: P060515-13 / References: UniProt: Q13114
#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: 1.10mM 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 / 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: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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