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- PDB-3hcs: Crystal structure of the N-terminal domain of TRAF6 -

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Basic information

Entry
Database: PDB / ID: 3hcs
TitleCrystal structure of the N-terminal domain of TRAF6
ComponentsTNF receptor-associated factor 6TRAF6
KeywordsSIGNALING PROTEIN / cross-brace / beta-beta-alpha / Coiled coil / Cytoplasm / Metal-binding / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger
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 / regulation of immunoglobulin production / ubiquitin conjugating enzyme binding / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / MyD88-dependent toll-like receptor signaling pathway / ubiquitin-ubiquitin ligase activity / toll-like receptor 4 signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / TRAF6 mediated IRF7 activation / T-helper 1 type immune response / cytoplasmic pattern recognition receptor signaling pathway / non-canonical NF-kappaB signal transduction / activation of protein kinase activity / cellular response to cytokine stimulus / odontogenesis of dentin-containing tooth / protein K63-linked ubiquitination / Fc-epsilon receptor signaling pathway / antiviral innate immune response / stimulatory C-type lectin receptor signaling pathway / TRAF6 mediated NF-kB activation / autophagosome assembly / positive regulation of type I interferon production / protein autoubiquitination / canonical NF-kappaB signal transduction / 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 / positive regulation of T cell proliferation / TICAM1,TRAF6-dependent induction of TAK1 complex / tumor necrosis factor-mediated signaling pathway / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-2 production / extrinsic component of cytoplasmic side of plasma membrane / TRAF6-mediated induction of TAK1 complex within TLR4 complex / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / positive regulation of interleukin-12 production / ossification / lipid droplet / 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 / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / cytoplasmic side of plasma membrane / CLEC7A (Dectin-1) signaling / positive regulation of T cell cytokine production / FCERI mediated NF-kB activation / protein polyubiquitination / positive regulation of interleukin-6 production / Interleukin-1 signaling / histone deacetylase binding / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / antigen processing and presentation of exogenous peptide antigen via MHC class II / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / Downstream TCR signaling / PIP3 activates AKT signaling / positive regulation of NF-kappaB transcription factor activity / cell cortex / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / cellular response to lipopolysaccharide
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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain ...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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsYin, Q. / Lin, S.-C. / Lamothe, B. / Lu, M. / Lo, Y.-C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. ...Yin, Q. / Lin, S.-C. / Lamothe, B. / Lu, M. / Lo, Y.-C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. / Lenardo, M.J. / Darnay, B.G. / Wu, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: E2 interaction and dimerization in the crystal structure of TRAF6.
Authors: Yin, Q. / Lin, S.C. / Lamothe, B. / Lu, M. / Lo, Y.C. / Hura, G. / Zheng, L. / Rich, R.L. / Campos, A.D. / Myszka, D.G. / Lenardo, M.J. / Darnay, B.G. / Wu, H.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)40,28212
Polymers39,6282
Non-polymers65410
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.663, 80.757, 50.723
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TNF receptor-associated factor 6 / TRAF6 / Interleukin-1 signal transducer / RING finger protein 85


Mass: 19813.875 Da / Num. of mol.: 2 / Fragment: RING and Zinc Fingers 1-3: UNP residues 50-211
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF85, TRAF6 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus RIPL / References: UniProt: Q9Y4K3
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.19-1.33M Ammonium sulfate, 0.1M CHES pH 9.4-9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH range: 9.4-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.2822 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 29, 2006 / Details: Mirrors
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2822 Å / Relative weight: 1
ReflectionRedundancy: 5.7 % / Av σ(I) over netI: 28.7 / Number: 169933 / Rmerge(I) obs: 0.074 / Χ2: 3.51 / D res high: 2.61 Å / D res low: 50 Å / Num. obs: 29792 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.625093.310.0463.9375.5
4.465.6296.610.0534.345.3
3.94.4697.210.0584.4935.3
3.543.998.910.0674.3025.6
3.293.5499.710.0883.8655.9
3.093.2999.810.123.3016.2
2.943.0999.910.163.0086.2
2.812.9410010.2182.8556.3
2.72.8110010.2872.6035.9
2.612.788.410.3592.5864.6
ReflectionResolution: 2.15→30 Å / Num. obs: 26445 / % possible obs: 98 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.074 / Χ2: 1.584 / Net I/σ(I): 28.703
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.485 / Num. unique all: 1087 / Χ2: 1.225 / % possible all: 81.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Occupancy max: 1.18 / Occupancy min: 0.93 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2321 9.1 %random
Rwork0.229 ---
obs0.229 23334 91.8 %-
Solvent computationBsol: 67.374 Å2
Displacement parametersBiso max: 95.53 Å2 / Biso mean: 50 Å2 / Biso min: 29.04 Å2
Baniso -1Baniso -2Baniso -3
1--13.293 Å20 Å2-4.901 Å2
2---2.547 Å20 Å2
3---15.841 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 10 196 2724
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2681.5
X-RAY DIFFRACTIONc_scbond_it2.1992
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scangle_it3.3312.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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