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- PDB-7l3l: Structure of TRAF5 and TRAF6 RING Hetero dimer -

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Basic information

Entry
Database: PDB / ID: 7l3l
TitleStructure of TRAF5 and TRAF6 RING Hetero dimer
Components
  • TNF receptor-associated factor 5
  • TNF receptor-associated factor 6TRAF6
KeywordsTRANSFERASE / E3 Ligase
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 / signal transduction involved in regulation of gene expression / Regulated proteolysis of p75NTR / activation of NF-kappaB-inducing kinase activity / mRNA stabilization / positive regulation of transcription regulatory region DNA binding / thioesterase 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 / interleukin-1-mediated 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 / activation of protein kinase activity / cellular response to cytokine stimulus / odontogenesis of dentin-containing tooth / protein K63-linked ubiquitination / non-canonical NF-kappaB signal transduction / 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 / 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 / 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 / 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 / positive regulation of JNK cascade / 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 / positive regulation of interleukin-6 production / Interleukin-1 signaling / protein polyubiquitination / 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
Similarity search - Function
TNF receptor-associated factor 5 / TNF receptor-associated factor TRAF / 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. ...TNF receptor-associated factor 5 / TNF receptor-associated factor TRAF / 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 finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 5 / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDas, A. / Middleton, A.J. / Padala, P. / Day, C.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: J.Mol.Biol. / Year: 2021
Title: The structure and ubiquitin binding properties of TRAF RING heterodimers.
Authors: Das, A. / Middleton, A.J. / Padala, P. / Ledgerwood, E.C. / Mace, P.D. / Day, C.L.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 5
B: TNF receptor-associated factor 6
C: TNF receptor-associated factor 5
D: TNF receptor-associated factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,75718
Polymers57,8414
Non-polymers91614
Water0
1
A: TNF receptor-associated factor 5
B: TNF receptor-associated factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3789
Polymers28,9202
Non-polymers4587
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: TNF receptor-associated factor 5
D: TNF receptor-associated factor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3789
Polymers28,9202
Non-polymers4587
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.597, 106.062, 94.427
Angle α, β, γ (deg.)90.00, 102.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TNF receptor-associated factor 5 / RING finger protein 84


Mass: 16589.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF5, RNF84 / Production host: Escherichia coli (E. coli) / References: UniProt: O00463
#2: 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: 12331.286 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 (E. coli)
References: UniProt: Q9Y4K3, RING-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8 / Details: 0.1 M Tris (pH 8), 0.2 M NaCl, 20 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→42.254 Å / Num. obs: 19772 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.04977 / Rpim(I) all: 0.04977 / Net I/σ(I): 13.49
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.4395 / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1970 / CC1/2: 0.53 / Rpim(I) all: 0.4395 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VO0

5vo0


Resolution: 2.8→42.25 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.71 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2335 956 4.84 %
Rwork0.2038 --
obs0.2102 19772 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 14 0 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043960
X-RAY DIFFRACTIONf_angle_d0.7985335
X-RAY DIFFRACTIONf_dihedral_angle_d21.7461514
X-RAY DIFFRACTIONf_chiral_restr0.049577
X-RAY DIFFRACTIONf_plane_restr0.005704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.94750.35611700.29632651X-RAY DIFFRACTION94
2.9475-3.13170.35291360.28962656X-RAY DIFFRACTION95
3.1317-3.37280.27911300.25612688X-RAY DIFFRACTION95
3.3728-3.7110.27941430.22422642X-RAY DIFFRACTION95
4.2452-5.33770.20671340.17472692X-RAY DIFFRACTION95

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