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- PDB-8hz2: Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-term... -

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Basic information

Entry
Database: PDB / ID: 8hz2
TitleTumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-terminal Domain
ComponentsTNF receptor-associated factor 6
KeywordsSIGNALING PROTEIN / TRAF6 / Zinc Finger Protein / Ubiquitin Ligase
Function / homology
Function and homology information


protein kinase B binding / interleukin-17A-mediated signaling pathway / positive regulation of transcription regulatory region DNA 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 ...protein kinase B binding / interleukin-17A-mediated signaling pathway / positive regulation of transcription regulatory region DNA 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 / toll-like receptor 3 signaling pathway / CD40 receptor complex / activation of protein kinase activity / myeloid dendritic cell differentiation / TRIF-dependent toll-like receptor signaling pathway / Regulated proteolysis of p75NTR / positive regulation of osteoclast differentiation / tumor necrosis factor receptor binding / positive regulation of lipopolysaccharide-mediated signaling pathway / regulation of immunoglobulin production / ubiquitin conjugating enzyme binding / extrinsic component of cytoplasmic side of plasma membrane / 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 / 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 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cytoplasmic pattern recognition receptor signaling pathway / 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 / positive regulation of T cell proliferation / protein autoubiquitination / signaling adaptor activity / lipid droplet / antiviral innate immune response / positive regulation of interleukin-12 production / 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-2 production / response to interleukin-1 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / osteoclast differentiation / NF-kB is activated and signals survival / ossification / NRIF signals cell death from the nucleus / lipopolysaccharide-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / 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 / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / cytoplasmic side of plasma membrane / histone deacetylase binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / positive regulation of NF-kappaB transcription factor activity / 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 / 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 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
Similarity search - Domain/homology
TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGuven, O. / Ciftci, H. / DeMirci, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Tumor Necrosis Factor Receptor Associated Factor 6 (TRAF6) N-terminal Domain
Authors: Guven, O. / Ciftci, H. / DeMirci, H.
History
DepositionJan 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
B: TNF receptor-associated factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,99212
Polymers36,3382
Non-polymers65410
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area19870 Å2
Unit cell
Length a, b, c (Å)45.885, 51.705, 54.300
Angle α, β, γ (deg.)91.04, 112.15, 108.43
Int Tables number1
Space group name H-MP1

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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: 18169.061 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6, RNF85 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9Y4K3, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.2 M Sodium Citrate Tribasic Dihydrate and 0.1 M TRIS 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Feb 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→5.998 Å / Num. obs: 12134 / % possible obs: 90.49 % / Redundancy: 1.5 % / CC1/2: 0.92 / Net I/σ(I): 3.12
Reflection shellResolution: 2.6→2.685 Å / Num. unique obs: 1157 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
CrysalisPro1.171.42.35adata reduction
CrysalisPro1.171.42.35adata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HCS

3hcs


Resolution: 2.6→5.998 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 50.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4086 1214 10.07 %
Rwork0.3479 --
obs0.3541 12052 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→5.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 10 46 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.538
X-RAY DIFFRACTIONf_dihedral_angle_d14.3371000
X-RAY DIFFRACTIONf_chiral_restr0.04366
X-RAY DIFFRACTIONf_plane_restr0.006468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.40911370.37571156X-RAY DIFFRACTION95
2.7-2.810.44091270.36641205X-RAY DIFFRACTION99
2.81-2.940.40631290.37181212X-RAY DIFFRACTION100
2.94-3.10.41421460.36961235X-RAY DIFFRACTION100
3.1-3.30.43981370.37341219X-RAY DIFFRACTION100
3.3-3.570.42051320.35441229X-RAY DIFFRACTION100
3.57-3.950.38991390.33161215X-RAY DIFFRACTION100
3.95-4.580.38971360.31591215X-RAY DIFFRACTION99
4.58-5.9980.40841310.34061152X-RAY DIFFRACTION94
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)
13.0833-0.18641.94132.16031.37314.03990.7521-0.7289-0.63540.85090.31230.58880.8931-0.74610.91930.4370.10010.05810.2069-0.18220.5001-22.540313.01314.8448
20.4962-0.2969-0.77421.85590.51781.22090.0704-0.28740.17740.50980.61960.3678-0.4527-0.6970.11260.5989-0.0772-0.05150.7254-0.00280.3586-23.00246.4964-3.6573
32.03650.475-0.00255.05830.87190.8696-0.6167-0.0257-0.0774-0.278-0.42720.63080.55310.42370.13830.6481-0.20540.08280.8551-0.07880.5627-27.2537.3221-10.6714
41.17411.08351.20484.6012.34464.34720.2076-0.1671-0.92560.41640.3508-0.9189-0.18090.05830.53530.40180.0505-0.04330.57560.10640.6744-18.21319.3775-10.9462
52.046-0.5635-0.21232.18580.80140.5090.4351-0.0098-0.16440.179-0.31710.89380.11940.3853-0.07760.47240.10340.090.60080.02440.5729-11.872713.59526.6218
61.1292-0.0476-0.57841.9665-2.3665.0258-0.4052-0.6026-0.34940.6987-0.4985-0.25150.1606-0.3656-0.13840.89640.13170.1720.666-0.00480.4827-22.57889.490122.7887
71.68130.21370.05313.874-0.11862.76910.3364-0.01480.08730.1743-0.4357-0.60410.30880.0107-0.06740.7553-0.1112-0.02380.36760.0021.0123-15.64896.688818.7742
81.1581-1.0592-0.23141.3827-0.88772.63870.55180.37610.5626-0.25410.20560.67890.05940.713-0.34930.5684-0.01610.0560.6041-0.0580.633-26.7649-7.547127.0604
94.73451.0389-0.53511.90980.71352.32760.0093-0.6447-1.359-0.3539-0.16690.21990.36780.00330.18640.4314-0.0552-0.00560.60510.02370.6842-29.5688-15.987237.4158
100.47310.15520.00491.62470.04640.4903-0.4505-0.0093-1.10650.021-0.34990.33130.51690.135-0.17750.55680.04440.4331.09520.18940.9256-38.4009-27.469343.8526
111.68560.40910.24080.8108-0.57362.02860.2429-0.0653-0.1436-0.1475-0.2722-0.00950.16270.0222-0.01290.3756-0.0741-0.04160.2572-0.04010.2949-6.946827.0557-4.8565
121.1825-0.0995-0.75710.1988-0.22731.06120.2757-0.7826-0.08410.3707-0.60980.6363-0.4841-0.23050.330.1007-0.2689-0.69970.6537-0.68081.07-6.697953.7697-16.8764
130.1466-0.1843-0.01050.159-0.03021.3314-0.6873-0.0828-0.63760.56660.33181.2284-0.06380.67890.20541.9020.34510.53662.11291.06481.6993-1.683669.5117-24.3895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 98 )
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 120 )
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 129 )
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 141 )
7X-RAY DIFFRACTION7chain 'A' and (resid 142 through 152 )
8X-RAY DIFFRACTION8chain 'A' and (resid 153 through 167 )
9X-RAY DIFFRACTION9chain 'A' and (resid 168 through 197 )
10X-RAY DIFFRACTION10chain 'A' and (resid 198 through 210 )
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 153 )
12X-RAY DIFFRACTION12chain 'B' and (resid 154 through 166 )
13X-RAY DIFFRACTION13chain 'B' and (resid 167 through 210 )

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