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- PDB-1ca4: STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2) -

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Basic information

Entry
Database: PDB / ID: 1ca4
TitleSTRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 (TRAF2)
ComponentsPROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
KeywordsTNF SIGNALING / TRAF / ADAPTER PROTEIN / CELL SURVIVAL
Function / homology
Function and homology information


CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 ...CD40 receptor binding / tumor necrosis factor receptor superfamily complex / sphingolipid binding / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / negative regulation of glial cell apoptotic process / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / tumor necrosis factor binding / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / interleukin-17-mediated signaling pathway / programmed necrotic cell death / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / CD40 receptor complex / signal transduction involved in regulation of gene expression / activation of NF-kappaB-inducing kinase activity / vesicle membrane / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / mRNA stabilization / thioesterase binding / tumor necrosis factor receptor binding / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to nitric oxide / regulation of protein-containing complex assembly / protein autoubiquitination / signaling adaptor activity / ubiquitin ligase complex / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-2 production / response to endoplasmic reticulum stress / 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 / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / positive regulation of T cell cytokine production / positive regulation of DNA-binding transcription factor activity / ubiquitin-protein transferase activity / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / protein-containing complex assembly / regulation of apoptotic process / protein phosphatase binding / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / Ub-specific processing proteases / membrane raft / innate immune response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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 / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. ...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 / 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 / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsPark, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H.
CitationJournal: Nature / Year: 1999
Title: Structural basis for self-association and receptor recognition of human TRAF2.
Authors: Park, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H.
History
DepositionFeb 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)


Theoretical massNumber of molelcules
Total (without water)114,0416
Polymers114,0416
Non-polymers00
Water13,385743
1
A: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
B: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
C: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)


Theoretical massNumber of molelcules
Total (without water)57,0213
Polymers57,0213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-23 kcal/mol
Surface area22700 Å2
MethodPISA
2
D: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
E: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)
F: PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2)


Theoretical massNumber of molelcules
Total (without water)57,0213
Polymers57,0213
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.920, 84.960, 124.070
Angle α, β, γ (deg.)90.00, 118.60, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

#1: Protein
PROTEIN (TNF RECEPTOR ASSOCIATED FACTOR 2) / TRAF2


Mass: 19006.916 Da / Num. of mol.: 6 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q12933
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 %PEG400011
20.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.992
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 57967 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.251 3531 5.6 %
Rwork0.209 --
obs-57967 92.7 %
Displacement parametersBiso mean: 22.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20 Å21.471 Å2
2---0.05 Å20 Å2
3---2.389 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 0 743 8435
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.71
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.1231.5
X-RAY DIFFRACTIONx_mcangle_it1.8832
X-RAY DIFFRACTIONx_scbond_it1.6692
X-RAY DIFFRACTIONx_scangle_it2.3992.5
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

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