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- PDB-3hct: Crystal structure of TRAF6 in complex with Ubc13 in the P1 space group -

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Basic information

Entry
Database: PDB / ID: 3hct
TitleCrystal structure of TRAF6 in complex with Ubc13 in the P1 space group
Components
  • TNF receptor-associated factor 6
  • Ubiquitin-conjugating enzyme E2 N
KeywordsSIGNALING PROTEIN/LIGASE / cross-brace / beta-beta-alpha / Coiled coil / Cytoplasm / Metal-binding / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger / ATP-binding / DNA damage / DNA repair / Isopeptide bond / Ligase / Nucleotide-binding / SIGNALING PROTEIN-LIGASE COMPLEX
Function / homology
Function and homology information


UBC13-MMS2 complex / protein kinase B binding / interleukin-17A-mediated signaling pathway / ubiquitin conjugating enzyme complex / positive regulation of transcription regulatory region DNA binding / ubiquitin-protein transferase activator activity / 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 ...UBC13-MMS2 complex / protein kinase B binding / interleukin-17A-mediated signaling pathway / ubiquitin conjugating enzyme complex / positive regulation of transcription regulatory region DNA binding / ubiquitin-protein transferase activator activity / 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 / positive regulation of protein K63-linked ubiquitination / 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 / regulation protein catabolic process at postsynapse / TRIF-dependent toll-like receptor signaling pathway / DNA double-strand break processing / 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 / postreplication repair / 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 / E2 ubiquitin-conjugating enzyme / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of double-strand break repair / 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 / ubiquitin conjugating enzyme activity / TRAF6 mediated NF-kB activation / positive regulation of intracellular signal transduction / positive regulation of JUN kinase activity / autophagosome assembly / protein K63-linked ubiquitination / canonical NF-kappaB signal transduction / protein monoubiquitination / positive regulation of type I interferon production / ubiquitin ligase complex / bone resorption / regulation of DNA repair / positive regulation of T cell proliferation / protein autoubiquitination / negative regulation of TORC1 signaling / 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 repair / positive regulation of DNA-binding transcription factor activity / TICAM1, RIP1-mediated IKK complex recruitment / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / neural tube closure / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / G2/M DNA damage checkpoint / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / positive regulation of T cell cytokine production
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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-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 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: TNF receptor-associated factor 6
B: Ubiquitin-conjugating enzyme E2 N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4125
Polymers31,2162
Non-polymers1963
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.985, 42.798, 49.118
Angle α, β, γ (deg.)104.610, 99.590, 108.600
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 13775.906 Da / Num. of mol.: 1 / Fragment: RING and Zinc Finger 1: UNP residues 50-159
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: Protein Ubiquitin-conjugating enzyme E2 N / Ubiquitin-protein ligase N / Ubiquitin carrier protein N / Ubc13 / Bendless-like ubiquitin-conjugating enzyme


Mass: 17440.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLU, UBE2N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon-Plus RIPL / References: UniProt: P61088, ubiquitin-protein ligase
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 14, 2007 / Details: Mirrors
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.06→30 Å / Num. obs: 16146 / % possible obs: 91.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.037 / Χ2: 3.715 / Net I/σ(I): 39.692
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.06-2.131.90.06515663.16691
2.13-2.221.90.05915763.64988.8
2.22-2.321.90.05216913.43995.8
2.32-2.441.90.04716913.62995.6
2.44-2.61.90.04416793.9195.2
2.6-2.81.90.04116653.99694.9
2.8-3.081.90.03716813.9294.9
3.08-3.521.90.03216643.66294.6
3.52-4.431.90.03416163.66691.9
4.43-301.90.03413174.18974.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2GMI, 3HCS

2gmi

3hcs


Resolution: 2.1→30 Å / Occupancy max: 1.17 / Occupancy min: 0.93 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.278 1498 9.2 %
Rwork0.212 --
obs0.212 14823 90.6 %
Solvent computationBsol: 79.746 Å2
Displacement parametersBiso max: 100.66 Å2 / Biso mean: 41.53 Å2 / Biso min: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1--7.774 Å2-2.913 Å2-6.478 Å2
2---7.216 Å211.51 Å2
3---14.989 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 3 195 2214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5571.5
X-RAY DIFFRACTIONc_scbond_it2.2192
X-RAY DIFFRACTIONc_mcangle_it2.5332
X-RAY DIFFRACTIONc_scangle_it3.3422.5
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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