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- PDB-5zuj: Binding and Enhanced Binding between Key Immunity Proteins TRAF6 ... -

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Basic information

Entry
Database: PDB / ID: 5zuj
TitleBinding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA
Components
  • TNF receptor-associated factor 6
  • peptide 170-184 from TRAF-interacting protein with FHA domain-containing protein A
KeywordsPROTEIN BINDING / Complex / TRAF6 / TIFA mutant peptide
Function / homology
Function and homology information


interleukin-17A-mediated signaling pathway / protein kinase B binding / CD40 signaling pathway / interleukin-17-mediated 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 / protein branched polyubiquitination / interleukin-33-mediated signaling pathway / CD40 receptor complex ...interleukin-17A-mediated signaling pathway / protein kinase B binding / CD40 signaling pathway / interleukin-17-mediated 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 / protein branched polyubiquitination / interleukin-33-mediated signaling pathway / CD40 receptor complex / toll-like receptor 3 signaling pathway / activation of protein kinase activity / 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 / TRAF6 mediated NF-kB activation / positive regulation of JUN kinase activity / autophagosome assembly / protein K63-linked ubiquitination / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / bone resorption / protein autoubiquitination / tumor necrosis factor-mediated signaling pathway / lipid droplet / signaling adaptor activity / positive regulation of T cell proliferation / positive regulation of interleukin-12 production / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / antiviral innate immune response / 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-2 production / p75NTR recruits signalling complexes / response to interleukin-1 / 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 / ossification / NRIF signals cell death from the nucleus / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / 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 / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / neural tube closure / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of NF-kappaB transcription factor activity / RING-type E3 ubiquitin transferase / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / protein homooligomerization / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / cytoplasmic side of plasma membrane / histone deacetylase binding / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / Downstream TCR signaling / 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
Similarity search - Function
TRAF-interacting protein with FHA domain-containing protein / 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 ...TRAF-interacting protein with FHA domain-containing protein / 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. / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Zinc finger, C3HC4 type (RING finger) / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRAF-interacting protein with FHA domain-containing protein A / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, W.C. / Maestre-Reyna, M. / Hsiao, T.C. / Tsai, M.D.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
MOST105-0210-01-12-01 Taiwan
MOST106-0210-01-15-04 Taiwan
MOST107-0210-01-19-02 Taiwan
CitationJournal: Chembiochem / Year: 2019
Title: Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA.
Authors: Huang, W.C. / Liao, J.H. / Hsiao, T.C. / Wei, T.W. / Maestre-Reyna, M. / Bessho, Y. / Tsai, M.D.
History
DepositionMay 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 6
I: peptide 170-184 from TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)20,4972
Polymers20,4972
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-1 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.518, 51.518, 335.679
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TNF receptor-associated factor 6 / E3 ubiquitin-protein ligase TRAF6 / Interleukin-1 signal transducer / RING finger protein 85 / RING- ...E3 ubiquitin-protein ligase TRAF6 / Interleukin-1 signal transducer / RING finger protein 85 / RING-type E3 ubiquitin transferase TRAF6


Mass: 18857.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6, RNF85 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y4K3, RING-type E3 ubiquitin transferase
#2: Protein/peptide peptide 170-184 from TRAF-interacting protein with FHA domain-containing protein A / TRAF2-binding protein


Mass: 1639.500 Da / Num. of mol.: 1 / Mutation: S174Q, M179D / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CG3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: 0.1 M HEPES sodium, pH 7.5, 1M Sodium citrate tribasic dihydrate, 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 19, 2017
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→44.62 Å / Num. obs: 9019 / % possible obs: 99.81 % / Redundancy: 1.96 % / Biso Wilson estimate: 49.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05055 / Rpim(I) all: 0.05055 / Rrim(I) all: 0.07149 / Net I/σ(I): 10.57
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 0.4142 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 863 / CC1/2: 0.777 / Rpim(I) all: 0.4142 / Rrim(I) all: 0.5858 / % possible all: 99.88

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHENIXmodel building
PHENIX1.12_2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LB5

1lb5


Resolution: 2.6→44.616 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.31
RfactorNum. reflection% reflection
Rfree0.2416 443 4.91 %
Rwork0.1929 --
obs0.1953 9015 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 0 63 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081362
X-RAY DIFFRACTIONf_angle_d1.0121846
X-RAY DIFFRACTIONf_dihedral_angle_d9.515820
X-RAY DIFFRACTIONf_chiral_restr0.058199
X-RAY DIFFRACTIONf_plane_restr0.006240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6930.29041310.24712750X-RAY DIFFRACTION100
2.693-3.74940.28491510.20382795X-RAY DIFFRACTION100
3.7494-44.62240.20661610.17353027X-RAY DIFFRACTION100

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