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- PDB-6a33: Binding and Enhanced Binding between Key Immunity Proteins TRAF6 ... -

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Basic information

Entry
Database: PDB / ID: 6a33
TitleBinding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA
Components
  • 15-mer peptide from TRAF-interacting protein with FHA domain-containing protein A
  • TNF receptor-associated factor 6TRAF6
KeywordsPROTEIN BINDING / Complex / TRAF6 / TIFA c-terminal consensus TRAF-binding peptide 170-184
Function / homology
Function and homology information


tumor necrosis factor receptor superfamily binding / protein kinase B binding / interleukin-17A-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 / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex ...tumor necrosis factor receptor superfamily binding / protein kinase B binding / interleukin-17A-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 / interleukin-17-mediated signaling pathway / interleukin-33-mediated signaling pathway / toll-like receptor 3 signaling pathway / CD40 receptor complex / positive regulation of lipopolysaccharide-mediated signaling pathway / myeloid dendritic cell differentiation / TRIF-dependent toll-like receptor signaling pathway / Regulated proteolysis of p75NTR / activation of NF-kappaB-inducing kinase activity / positive regulation of transcription regulatory region DNA binding / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / ubiquitin conjugating enzyme binding / regulation of immunoglobulin production / regulation of canonical NF-kappaB signal transduction / MyD88-dependent toll-like receptor signaling pathway / ubiquitin-ubiquitin ligase activity / interleukin-1-mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / TRAF6 mediated IRF7 activation / T-helper 1 type immune response / cytoplasmic pattern recognition receptor signaling pathway / activation of protein kinase activity / odontogenesis of dentin-containing tooth / non-canonical NF-kappaB signal transduction / protein K63-linked ubiquitination / cellular response to cytokine stimulus / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / antiviral innate immune response / TRAF6 mediated NF-kB activation / autophagosome assembly / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / protein autoubiquitination / positive regulation of JUN kinase activity / bone resorption / lipopolysaccharide-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 T cell proliferation / tumor necrosis factor-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / extrinsic component of cytoplasmic side of plasma membrane / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interleukin-2 production / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / lipid droplet / ossification / response to interleukin-1 / TICAM1, RIP1-mediated IKK complex recruitment / osteoclast differentiation / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of protein ubiquitination / Regulation of NF-kappa B signaling / neural tube closure / activated TAK1 mediates p38 MAPK activation / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / protein homooligomerization / cytoplasmic side of plasma membrane / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / positive regulation of DNA-binding transcription factor activity / positive regulation of interleukin-6 production / histone deacetylase binding / 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 / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / regulation of apoptotic process / in utero embryonic development
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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : ...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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain / 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: 2.1 Å
AuthorsHuang, W.C. / Liao, J.H. / Hsiao, T.C. / Maestre-Reyna, M. / Bessho, Y. / 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
DepositionJun 14, 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

Downloads & links

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Assembly

Deposited unit
A: TNF receptor-associated factor 6
I: 15-mer peptide from TRAF-interacting protein with FHA domain-containing protein A


Theoretical massNumber of molelcules
Total (without water)20,4722
Polymers20,4722
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-1 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.430, 51.430, 336.570
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 / TRAF6 / 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 15-mer peptide from TRAF-interacting protein with FHA domain-containing protein A / Putative MAPK-activating protein PM14 / Putative NF-kappa-B-activating protein 20 / TRAF2-binding protein


Mass: 1614.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CG3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 60.81 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5
Details: 0.1 M HEPES sodium, pH 7.5, 1M Sodium citrate tribasic dihydrate, and 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 7, 2017 / Details: K-B mirrors
RadiationMonochromator: liquid nitrogen cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.4 Å / Num. obs: 16418 / % possible obs: 98.4 % / Redundancy: 1.99963 % / Biso Wilson estimate: 40.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0198 / Rpim(I) all: 0.0198 / Rrim(I) all: 0.028 / Net I/σ(I): 16.43
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3512 / Num. unique obs: 1576 / CC1/2: 0.827 / Rpim(I) all: 0.3512 / Rrim(I) all: 0.4967 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PHENIX1.12_2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZUJ

5zuj


Resolution: 2.1→41.397 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2468 820 5 %
Rwork0.1937 --
obs0.1963 16399 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 0 124 1421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061339
X-RAY DIFFRACTIONf_angle_d0.8451818
X-RAY DIFFRACTIONf_dihedral_angle_d11.2961103
X-RAY DIFFRACTIONf_chiral_restr0.054196
X-RAY DIFFRACTIONf_plane_restr0.005237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.23160.29721310.24932518X-RAY DIFFRACTION98
2.2316-2.40390.30661300.22452463X-RAY DIFFRACTION98
2.4039-2.64580.25661330.22232523X-RAY DIFFRACTION98
2.6458-3.02860.2351360.20672578X-RAY DIFFRACTION98
3.0286-3.81520.30751380.18252615X-RAY DIFFRACTION99
3.8152-41.40470.20541520.17952882X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.95590.1815-1.7471.2684-0.61856.1710.05660.24110.33920.20550.03360.171-0.68910.0393-0.06640.46980.0037-0.00710.23770.02340.320916.387927.343-12.0524
23.69751.4121-3.31780.8366-2.21426.0391-0.0589-0.1018-0.28910.0608-0.0712-0.1233-0.10860.43050.17120.4555-0.01360.02360.3019-0.03140.301212.575418.7164-8.6114
33.02520.2747-1.69472.5487-3.82947.7606-0.2796-0.2773-0.29170.03380.1027-0.03380.259-0.20940.1860.42610.00410.05720.2386-0.01310.27295.830613.4332-1.5571
43.5386-0.09070.48444.2533-1.91045.7425-0.0128-0.0269-0.1924-0.07620.0640.25290.4904-0.3651-0.02470.33760.030.10580.2871-0.04470.27746.108715.4178-9.2906
52.3530.82050.42043.2606-2.56846.2797-0.02890.04360.21260.13540.13210.3462-0.4249-0.2027-0.14810.39050.01030.06840.2868-0.00290.31777.636824.4026-16.993
63.6935-0.83030.18282.7731-1.4933.7625-0.36540.21850.6496-0.51620.2391-1.2137-0.08421.9677-0.28880.89340.06120.11610.7622-0.12670.663316.03329.4524-10.8676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 350 through 376 )
2X-RAY DIFFRACTION2chain 'A' and (resid 377 through 406 )
3X-RAY DIFFRACTION3chain 'A' and (resid 407 through 434 )
4X-RAY DIFFRACTION4chain 'A' and (resid 435 through 470 )
5X-RAY DIFFRACTION5chain 'A' and (resid 471 through 501 )
6X-RAY DIFFRACTION6chain 'I' and (resid 174 through 184 )

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