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- PDB-2jmd: Solution Structure of the Ring Domain of Human TRAF6 -

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Basic information

Entry
Database: PDB / ID: 2jmd
TitleSolution Structure of the Ring Domain of Human TRAF6
ComponentsTNF receptor-associated factor 6
KeywordsLIGASE / Protein / Zinc-binding / human TNF receptor-associated factor 6 / Zn2+ coordination
Function / homology
Function and homology information


interleukin-17A-mediated signaling pathway / protein kinase B binding / CD40 signaling pathway / MyD88 dependent cascade initiated on endosome / 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 / activation of protein kinase activity / protein branched polyubiquitination / interleukin-33-mediated signaling pathway ...interleukin-17A-mediated signaling pathway / protein kinase B binding / CD40 signaling pathway / MyD88 dependent cascade initiated on endosome / 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 / activation of protein kinase activity / protein branched polyubiquitination / interleukin-33-mediated signaling pathway / CD40 receptor complex / toll-like receptor 3 signaling pathway / TRIF-dependent toll-like receptor signaling pathway / Regulated proteolysis of p75NTR / myeloid dendritic cell differentiation / positive regulation of osteoclast differentiation / positive regulation of lipopolysaccharide-mediated signaling pathway / tumor necrosis factor receptor binding / regulation of immunoglobulin production / ubiquitin conjugating enzyme binding / non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / MyD88-dependent toll-like receptor signaling pathway / TRAF6 mediated IRF7 activation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / T-helper 1 type immune response / toll-like receptor 4 signaling pathway / ubiquitin-ubiquitin ligase activity / cytoplasmic pattern recognition receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cellular response to cytokine stimulus / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / odontogenesis of dentin-containing tooth / positive regulation of JUN kinase activity / TRAF6 mediated NF-kB activation / autophagosome assembly / protein K63-linked ubiquitination / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / bone resorption / 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 / p75NTR recruits signalling complexes / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / protein autoubiquitination / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / lipid droplet / signaling adaptor activity / positive regulation of T cell proliferation / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-12 production / antiviral innate immune response / positive regulation of interleukin-2 production / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / response to interleukin-1 / ossification / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / tumor necrosis factor-mediated signaling pathway / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / neural tube closure / positive regulation of JNK cascade / CLEC7A (Dectin-1) signaling / positive regulation of NF-kappaB transcription factor activity / FCERI mediated NF-kB activation / positive regulation of T cell cytokine production / RING-type E3 ubiquitin transferase / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interleukin-1 signaling / positive regulation of interleukin-6 production / SARS-CoV-1 activates/modulates innate immune responses / cytoplasmic side of plasma membrane / histone deacetylase binding / Ovarian tumor domain proteases / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / ubiquitin protein ligase activity / PIP3 activates AKT signaling / T cell receptor signaling pathway / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell cortex / protein-macromolecule adaptor activity / regulation of apoptotic process
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, simulated annealing
AuthorsMercier, P. / Lewis, M.J. / Hau, D.D. / Saltibus, L.F. / Xiao, W. / Spyracopoulos, L.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure, interactions, and dynamics of the RING domain from human TRAF6
Authors: Mercier, P. / Lewis, M.J. / Hau, D.D. / Saltibus, L.F. / Xiao, W. / Spyracopoulos, L.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,1453
Polymers7,0141
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)50 / 50all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein TNF receptor-associated factor 6 / Interleukin 1 signal transducer / RING finger protein 85 / hTRAF6


Mass: 7014.247 Da / Num. of mol.: 1 / Fragment: RING-type domain, residues 66-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6, RNF85 / Production host: Escherichia coli (E. coli) / Strain (production host): BL23DE3 / 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 HNCO
1213D HNCA
1313D HN(CA)CB
1413D HNHA
1513D HNHB
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1912D 1H-13C HSQC
11012D 1H-15N HSQC
11113D HACA(CO)CANHh
11213D H(CC)-TOCSY-(CO)NNH
11313D (H)CCTOCSY(CO)NNH
11412D (HB)CB(CGCD)HD
11512D (HB)CB(CGCDCE)HE
11613D HNN(CO,CA)

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C, U-99% 15N] hTRAF6, 50 mM phosphate, 150 mM NaCl, pH 7.5, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: hTRAF6 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.2 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRView6.5Johnsonstructure solution
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
X-PLOR NIH2.15Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.15Schwieters, Kuszewski, Tjandra and Clorestructure solution
VnmrJ2.1Variancollection
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Cyana's internal protocol and refinement of Cyana's structures in explicit solvent using XPLOR-NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 50 / Conformers submitted total number: 50 / Maximum lower distance constraint violation: 0.3 Å / Maximum upper distance constraint violation: 0.1 Å

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