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- PDB-2eci: Solution structure of the RING domain of the human TNF receptor-a... -

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Basic information

Entry
Database: PDB / ID: 2eci
TitleSolution structure of the RING domain of the human TNF receptor-associated factor 6 protein
ComponentsTNF receptor-associated factor 6
KeywordsMETAL BINDING PROTEIN / TNF receptor-associated factor 6 / TRAF6 / RING domain / zinc-binding domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein kinase B binding / interleukin-17A-mediated signaling pathway / MyD88 dependent cascade initiated on endosome / CD40 signaling pathway / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex ...protein kinase B binding / interleukin-17A-mediated signaling pathway / MyD88 dependent cascade initiated on endosome / CD40 signaling pathway / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex / positive regulation of transcription regulatory region DNA binding / positive regulation of lipopolysaccharide-mediated signaling pathway / TRIF-dependent toll-like receptor signaling pathway / myeloid dendritic cell differentiation / Regulated proteolysis of p75NTR / tumor necrosis factor receptor binding / positive regulation of osteoclast differentiation / regulation of immunoglobulin production / ubiquitin conjugating enzyme binding / regulation of canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / non-canonical NF-kappaB signal transduction / ubiquitin-ubiquitin ligase activity / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / cytoplasmic pattern recognition receptor signaling pathway / T-helper 1 type immune response / activation of protein kinase activity / stimulatory C-type lectin receptor signaling pathway / cellular response to cytokine stimulus / extrinsic component of cytoplasmic side of plasma membrane / odontogenesis of dentin-containing tooth / Fc-epsilon receptor signaling pathway / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / autophagosome assembly / positive regulation of type I interferon production / protein autoubiquitination / bone resorption / canonical NF-kappaB signal transduction / positive regulation of T cell proliferation / antiviral innate immune response / positive regulation of JUN kinase activity / lipopolysaccharide-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / positive regulation of interleukin-12 production / positive regulation of interleukin-2 production / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / NF-kB is activated and signals survival / response to interleukin-1 / NRIF signals cell death from the nucleus / ossification / osteoclast differentiation / lipid droplet / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / neural tube closure / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / positive regulation of DNA-binding transcription factor activity / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / histone deacetylase binding / FCERI mediated NF-kB activation / positive regulation of interleukin-6 production / cytoplasmic side of plasma membrane / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / antigen processing and presentation of exogenous peptide antigen via MHC class II / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Downstream TCR signaling / PIP3 activates AKT signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / protein-macromolecule adaptor activity / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cellular response to lipopolysaccharide / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development
Similarity search - Function
TNF receptor-associated factor 6, zinc finger 2 / TNF receptor-associated factor 6 zinc finger 2 / TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. ...TNF receptor-associated factor 6, zinc finger 2 / TNF receptor-associated factor 6 zinc finger 2 / TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Zinc finger, C3HC4 type (RING finger) / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K. / Sato, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the RING domain of the human TNF receptor-associated factor 6 protein
Authors: Miyamoto, K. / Sato, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 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:
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Assembly

Deposited unit
A: TNF receptor-associated factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7463
Polymers9,6151
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 6 / Interleukin 1 signal transducer / RING finger protein 85


Mass: 9614.990 Da / Num. of mol.: 1 / Fragment: RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TRAF6 / Plasmid: P060613-08 / References: UniProt: Q9Y4K3
#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 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.08mM RING domain 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: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, 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, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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