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- PDB-2gkw: Key contacts promote recongnito of BAFF-R by TRAF3 -

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Basic information

Entry
Database: PDB / ID: 2gkw
TitleKey contacts promote recongnito of BAFF-R by TRAF3
Components
  • TNF receptor-associated factor 3
  • Tumor necrosis factor receptor superfamily member 13C
KeywordsAPOPTOSIS / CD40 / NF-kB signaling / BAFF receptor / TRAF3
Function / homology
Function and homology information


regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / serine/threonine protein kinase complex / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / regulation of proteolysis / thioesterase binding ...regulation of interferon-beta production / TRAF3 deficiency - HSE / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / serine/threonine protein kinase complex / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / regulation of proteolysis / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / type I interferon-mediated signaling pathway / protein K63-linked ubiquitination / positive regulation of type I interferon production / ubiquitin ligase complex / tumor necrosis factor-mediated signaling pathway / regulation of cytokine production / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / RING-type E3 ubiquitin transferase / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Ovarian tumor domain proteases / TRAF3-dependent IRF activation pathway / protein phosphatase binding / defense response to virus / regulation of apoptotic process / endosome membrane / endosome / ubiquitin protein ligase binding / protein kinase binding / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING 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 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEly, K.R.
CitationJournal: J.Immunol. / Year: 2004
Title: Key molecular contacts promote recognition of the BAFF receptor by TNF receptor-associated factor 3: implications for intracellular signaling regulation.
Authors: Ni, C.-Z. / Oganesyan, G. / Welsh, K. / Zhu, X. / Reed, J.C. / Satterthwait, A.C. / Cheng, G. / Ely, K.R.
History
DepositionApr 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 3
B: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)24,2472
Polymers24,2472
Non-polymers00
Water00
1
A: TNF receptor-associated factor 3
B: Tumor necrosis factor receptor superfamily member 13C

A: TNF receptor-associated factor 3
B: Tumor necrosis factor receptor superfamily member 13C

A: TNF receptor-associated factor 3
B: Tumor necrosis factor receptor superfamily member 13C


Theoretical massNumber of molelcules
Total (without water)72,7406
Polymers72,7406
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13630 Å2
ΔGint-70 kcal/mol
Surface area27490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.5, 83.5, 78.0
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein TNF receptor-associated factor 3 / CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein ...CD40 receptor-associated factor 1 / CRAF1 / CD40-binding protein / CD40BP / LMP1-associated protein / LAP1 / CAP-1


Mass: 21833.135 Da / Num. of mol.: 1 / Fragment: TRAF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAF3, CAP1, CRAF1 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13114
#2: Protein/peptide Tumor necrosis factor receptor superfamily member 13C / BAFF Receptor / B cell-activating factor receptor / BAFF-R / BLyS receptor 3 / B-cell maturation defect


Mass: 2413.651 Da / Num. of mol.: 1 / Fragment: Residues 160-183 / Source method: obtained synthetically
Details: The sequence of this protein naturally exists in Homo Sapiens (Human).

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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: 3.24 Å3/Da / Density % sol: 61.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 4000, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 8920 / Num. obs: 8860 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 80.3

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Processing

Software
NameVersionClassification
CNS1refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1FLL

1fll


Resolution: 2.7→14.85 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 309645.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 438 5.4 %RANDOM
Rwork0.22 ---
obs0.22 8072 90.6 %-
all-8910 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.7415 Å2 / ksol: 0.374209 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-8 Å
Luzzati sigma a0.4 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 0 1650
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it3.322
X-RAY DIFFRACTIONc_scangle_it4.362.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.423 62 5.3 %
Rwork0.315 1104 -
obs-1104 80.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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