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- PDB-1lb4: TRAF6 apo structure -

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Basic information

Entry
Database: PDB / ID: 1lb4
TitleTRAF6 apo structure
ComponentsTNF receptor-associated factor 6TRAF6
KeywordsSIGNALING PROTEIN / apo form
Function / homology
Function and homology information


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 ...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 / activation of protein kinase activity / cytoplasmic pattern recognition receptor signaling pathway / non-canonical NF-kappaB signal transduction / odontogenesis of dentin-containing tooth / 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 T cell proliferation / positive regulation of JUN kinase activity / bone resorption / lipopolysaccharide-mediated signaling pathway / extrinsic component of cytoplasmic side of plasma membrane / 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 / tumor necrosis factor-mediated signaling pathway / TICAM1,TRAF6-dependent induction of TAK1 complex / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of interleukin-2 production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / response to interleukin-1 / lipid droplet / ossification / 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 / positive regulation of T cell cytokine production / CLEC7A (Dectin-1) signaling / positive regulation of DNA-binding transcription factor activity / histone deacetylase binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of interleukin-6 production / 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 / T cell receptor signaling pathway / cell cortex / 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 / endosome membrane
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 / 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 / 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
TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYe, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O. / Vologodskaia, M. / Yim, M. ...Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O. / Vologodskaia, M. / Yim, M. / Du, K. / Singh, S. / Pike, J.W. / Darnay, B.G. / Choi, Y. / Wu, H.
CitationJournal: Nature / Year: 2002
Title: Distinct molecular mechanism for initiating TRAF6 signalling.
Authors: Ye, H. / Arron, J.R. / Lamothe, B. / Cirilli, M. / Kobayashi, T. / Shevde, N.K. / Segal, D. / Dzivenu, O.K. / Vologodskaia, M. / Yim, M. / Du, K. / Singh, S. / Pike, J.W. / Darnay, B.G. / Choi, Y. / Wu, H.
History
DepositionApr 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor-associated factor 6


Theoretical massNumber of molelcules
Total (without water)18,5481
Polymers18,5481
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.183, 55.581, 47.709
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TNF receptor-associated factor 6 / TRAF6


Mass: 18548.420 Da / Num. of mol.: 1 / Fragment: residues 348-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y4K3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-25 %PEG800011
2100 mMTris-HCl11pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 7809 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 8.4 Å2 / Rsym value: 0.092
Reflection shellResolution: 2.4→2.55 Å / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.241

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRAF2

Resolution: 2.4→31.6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 666 -RANDOM
Rwork0.204 ---
obs-6283 10.6 %-
Displacement parametersBiso mean: 22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 0 45 1314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.84
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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