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- PDB-3knv: Crystal structure of the RING and first zinc finger domains of TRAF2 -

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Basic information

Entry
Database: PDB / ID: 3knv
TitleCrystal structure of the RING and first zinc finger domains of TRAF2
ComponentsTNF receptor-associated factor 2
KeywordsSIGNALING PROTEIN / Cross-brace / Alternative splicing / Apoptosis / Cytoplasm / Metal-binding / Ubl conjugation / Zinc / Zinc-finger
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 / mitogen-activated protein kinase kinase kinase binding / positive regulation of tumor necrosis factor-mediated signaling pathway / thioesterase binding / tumor necrosis factor receptor binding / mRNA stabilization / positive regulation of extrinsic apoptotic signaling pathway / regulation of immunoglobulin production / vesicle membrane / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / 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 / RING-type E3 ubiquitin transferase / protein catabolic process / 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 / positive regulation of NF-kappaB transcription factor activity / protein-macromolecule adaptor activity / cell cortex / protein-containing complex assembly / protein phosphatase binding / regulation of apoptotic process / 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 / cytosol / cytoplasm
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 / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TNF receptor-associated factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsYin, Q. / Wu, H.
CitationJournal: Biochemistry / Year: 2009
Title: Structural basis for the lack of E2 interaction in the RING domain of TRAF2.
Authors: Yin, Q. / Lamothe, B. / Darnay, B.G. / Wu, H.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: TNF receptor-associated factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6024
Polymers15,4061
Non-polymers1963
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.669, 43.669, 284.393
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-174-

HOH

DetailsThe molecule exists in solution mainly as a dimer. The two-fold axis coincides with a crystallographic two-fold axis. Therefore, the asymmetric unit contains half of the biological unit.

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Components

#1: Protein TNF receptor-associated factor 2 / Tumor necrosis factor type 2 receptor-associated protein 3


Mass: 15405.579 Da / Num. of mol.: 1
Fragment: RING and the first zinc finger domains: UNP residues 1-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF2, TRAP3 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIPL / References: UniProt: Q12933
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 8000, 0.1 M HEPES pH 7.5, 8% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2008
Details: Sagitally focused second crystal. Two spherical mirrors, one rhodium coated
RadiationMonochromator: KOHZU double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 23319 / % possible obs: 99 % / Redundancy: 22.9 % / Rmerge(I) obs: 0.074 / Χ2: 1.992 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.83-1.866.30.3316100.90784.7
1.86-1.912.80.3717750.82599.7
1.9-1.9314.80.3417040.77999.6
1.93-1.9715.70.3167530.86899.6
1.97-2.0116.40.2877360.97399.6
2.01-2.0617.80.277531.04799.6
2.06-2.1118.20.2537421.10399.5
2.11-2.1719.40.2427601.2199.9
2.17-2.2319.60.2167481.278100
2.23-2.3120.60.1947711.433100
2.31-2.3920.40.187431.61100
2.39-2.4820.40.1547621.757100
2.48-2.620.50.1487731.74899.9
2.6-2.7320.10.1367922.12799.9
2.73-2.920.30.1217762.313100
2.9-3.1337.40.0967892.445100
3.13-3.4439.40.0827802.723100
3.44-3.9438.80.0678152.933100
3.94-4.97370.0588332.89399.5
4.97-50320.0499512.58797.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.8 Å / Occupancy max: 1.23 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.239 2196 9.2 %
Rwork0.216 --
obs0.216 23319 97.6 %
Solvent computationBsol: 58.397 Å2
Displacement parametersBiso max: 84.12 Å2 / Biso mean: 37.527 Å2 / Biso min: 18.79 Å2
Baniso -1Baniso -2Baniso -3
1-5.938 Å20 Å20 Å2
2--5.938 Å20 Å2
3----11.875 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 3 92 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4261.5
X-RAY DIFFRACTIONc_scbond_it2.1752
X-RAY DIFFRACTIONc_mcangle_it2.2352
X-RAY DIFFRACTIONc_scangle_it3.3652.5
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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