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- PDB-5h10: TRAF1-TANk complex -

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Basic information

Entry
Database: PDB / ID: 5h10
TitleTRAF1-TANk complex
Components
  • TNF receptor-associated factor 1
  • TRAF family member-associated NF-kappaB activator
KeywordsSIGNALING PROTEIN/INHIBITOR / TRAF / TANK / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of extrinsic apoptotic signaling pathway / positive regulation of protein deubiquitination / positive regulation of ubiquitin-specific protease activity / serine/threonine protein kinase complex / thioesterase binding / deubiquitinase activator activity / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / TRAF6 mediated IRF7 activation / molecular function inhibitor activity ...regulation of extrinsic apoptotic signaling pathway / positive regulation of protein deubiquitination / positive regulation of ubiquitin-specific protease activity / serine/threonine protein kinase complex / thioesterase binding / deubiquitinase activator activity / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / TRAF6 mediated IRF7 activation / molecular function inhibitor activity / type I interferon-mediated signaling pathway / protein K63-linked ubiquitination / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / negative regulation of canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / TICAM1-dependent activation of IRF3/IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / TNFR1-induced NF-kappa-B signaling pathway / cellular response to ionizing radiation / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / protein-containing complex assembly / defense response to virus / molecular adaptor activity / apoptotic process / ubiquitin protein ligase binding / DNA damage response / signal transduction / protein-containing complex / zinc ion binding / identical protein binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
TNF receptor-associated factor 1, MATH domain / TRAF family member-associated NF-kappa-B activator / Tbk1/Ikki binding domain / TBD domain / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / TNF receptor-associated factor TRAF, metazoa / : ...TNF receptor-associated factor 1, MATH domain / TRAF family member-associated NF-kappa-B activator / Tbk1/Ikki binding domain / TBD domain / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TNF receptor-associated factor 1 / TRAF family member-associated NF-kappa-B activator
Similarity search - Component
Biological speciesHomo sapiens (human)
Peptide display vector fth1 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.205 Å
AuthorsKim, C.M. / Park, H.H.
CitationJournal: To Be Published
Title: TRAF1-TANk complex
Authors: Kim, C.M. / Park, H.H.
History
DepositionOct 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: TNF receptor-associated factor 1
B: TNF receptor-associated factor 1
C: TNF receptor-associated factor 1
D: TRAF family member-associated NF-kappaB activator
E: TRAF family member-associated NF-kappaB activator
F: TRAF family member-associated NF-kappaB activator


Theoretical massNumber of molelcules
Total (without water)73,7376
Polymers73,7376
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-80 kcal/mol
Surface area30810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.210, 79.034, 113.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TNF receptor-associated factor 1 / Epstein-Barr virus-induced protein 6


Mass: 23717.104 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF1, EBI6
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q13077
#2: Protein/peptide TRAF family member-associated NF-kappaB activator / TANK peptide


Mass: 861.960 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Peptide display vector fth1 (others) / References: UniProt: Q92844*PLUS

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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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.38M Ammonium sulfate, 0.1M CHES pH 9.3, 200mM NaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 11811 / % possible obs: 99.5 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.065 / Rsym value: 0.067 / Net I/σ(I): 42.34
Reflection shellResolution: 3.2→3.25 Å / Rmerge(I) obs: 0.172 / Rsym value: 0.182

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E1T

5e1t


Resolution: 3.205→29.89 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 27.58
RfactorNum. reflection% reflection
Rfree0.2698 1176 9.98 %
Rwork0.2183 --
obs0.2235 11785 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.205→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 0 4808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024906
X-RAY DIFFRACTIONf_angle_d0.5176622
X-RAY DIFFRACTIONf_dihedral_angle_d13.232984
X-RAY DIFFRACTIONf_chiral_restr0.036739
X-RAY DIFFRACTIONf_plane_restr0.003849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2055-3.35120.31721420.24841269X-RAY DIFFRACTION96
3.3512-3.52760.29371440.24691294X-RAY DIFFRACTION100
3.5276-3.74820.26571390.22421310X-RAY DIFFRACTION99
3.7482-4.0370.27291500.22811299X-RAY DIFFRACTION100
4.037-4.44210.2321410.1941339X-RAY DIFFRACTION100
4.4421-5.08210.23471470.19661329X-RAY DIFFRACTION100
5.0821-6.39260.25761540.23531347X-RAY DIFFRACTION100
6.3926-29.89160.30391590.21611422X-RAY DIFFRACTION100

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