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- PDB-1f3v: Crystal structure of the complex between the N-terminal domain of... -

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Basic information

Entry
Database: PDB / ID: 1f3v
TitleCrystal structure of the complex between the N-terminal domain of TRADD and the TRAF domain of TRAF2
Components
  • TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN
  • TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN
KeywordsAPOPTOSIS / a-b sandwich
Function / homology
Function and homology information


TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / death domain binding / sphingolipid binding / TRAF2-GSTP1 complex / IRE1-TRAF2-ASK1 complex / CD27 signaling pathway / positive regulation of hair follicle development ...TORC2 complex disassembly / CD40 receptor binding / TORC1 complex assembly / tumor necrosis factor receptor superfamily complex / death domain binding / sphingolipid binding / TRAF2-GSTP1 complex / IRE1-TRAF2-ASK1 complex / CD27 signaling pathway / positive regulation of hair follicle development / Defective RIPK1-mediated regulated necrosis / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / CD40 signaling pathway / tumor necrosis factor binding / TRAIL-activated apoptotic signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / interleukin-17-mediated signaling pathway / negative regulation of glial cell apoptotic process / TNF signaling / CD40 receptor complex / programmed necrotic cell death / Caspase activation via Death Receptors in the presence of ligand / death-inducing signaling complex / transmembrane receptor protein tyrosine kinase adaptor activity / thioesterase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / tumor necrosis factor receptor binding / mRNA stabilization / regulation of immunoglobulin production / non-canonical NF-kappaB signal transduction / vesicle membrane / regulation of JNK cascade / positive regulation of extrinsic apoptotic signaling pathway / mitogen-activated protein kinase kinase kinase binding / signal transduction involved in regulation of gene expression / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / RIPK1-mediated regulated necrosis / positive regulation of JUN kinase activity / TRAF6 mediated NF-kB activation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / protein K63-linked ubiquitination / canonical NF-kappaB signal transduction / ubiquitin ligase complex / regulation of protein-containing complex assembly / protein autoubiquitination / extrinsic apoptotic signaling pathway / signaling adaptor activity / positive regulation of interleukin-2 production / cellular response to nitric oxide / response to endoplasmic reticulum stress / T cell activation / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / protein catabolic process / positive regulation of NF-kappaB transcription factor activity / positive regulation of T cell cytokine production / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / kinase binding / cytoplasmic side of plasma membrane / positive regulation of inflammatory response / ubiquitin-protein transferase activity / cellular response to tumor necrosis factor / ubiquitin protein ligase activity / protein-containing complex assembly / cell cortex / protein phosphatase binding / protein-macromolecule adaptor activity / regulation of apoptotic process / cytoskeleton / positive regulation of canonical NF-kappaB signal transduction / receptor complex / Ub-specific processing proteases / positive regulation of cell migration / positive regulation of apoptotic process / membrane raft / innate immune response / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex binding / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
TRADD, N-terminal domain / TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / TNF receptor-associated factor, BIRC3 binding domain ...TRADD, N-terminal domain / TRADD, N-terminal / TRADD / TRADD, N-terminal domain superfamily / TRADD, N-terminal domain / TNF receptor-associated factor 2 / TNF receptor-associated factor 2, MATH domain / : / TRAF2, second zinc finger / TNF receptor-associated factor, BIRC3 binding domain / TNF receptor-associated factor BIRC3 binding domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / 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 / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TNF receptor-associated factor 2 / Tumor necrosis factor receptor type 1-associated DEATH domain protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsPark, Y.C. / Ye, H. / Hsia, C. / Segal, D. / Rich, R. / Liou, H.-C. / Myszka, D. / Wu, H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: A novel mechanism of TRAF signaling revealed by structural and functional analyses of the TRADD-TRAF2 interaction.
Authors: Park, Y.C. / Ye, H. / Hsia, C. / Segal, D. / Rich, R.L. / Liou, H.C. / Myszka, D.G. / Wu, H.
History
DepositionJun 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 16, 2012Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN
B: TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)39,1322
Polymers39,1322
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.4, 132.4, 62.8
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TUMOR NECROSIS FACTOR RECEPTOR TYPE 1 ASSOCIATED DEATH DOMAIN PROTEIN / TRADD / TNFR1-ASSOCIATED DEATH DOMAIN PROTEIN


Mass: 19412.998 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q15628
#2: Protein TUMOR NECROSIS FACTOR RECEPTOR-ASSOCIATED PROTEIN / TRAF2


Mass: 19718.646 Da / Num. of mol.: 1 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q12933
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %PEG40001reservoir
24 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9
DetectorType: ADSC / Detector: CCD / Date: Jun 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→20 Å
Reflection
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.036

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / σ(F): 2 /
Rfactor% reflection
Rfree0.261 -
Rwork0.229 -
obs-99 %
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 0 208 2749
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.7

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