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- PDB-1flk: MOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3 -

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Basic information

Entry
Database: PDB / ID: 1flk
TitleMOLECULAR BASIS FOR CD40 SIGNALING MEDIATED BY TRAF3
ComponentsTNF RECEPTOR ASSOCIATED FACTOR 3
KeywordsAPOPTOSIS / TNF SIGNALING / TRAF3 / CD40-BINDING PROTEIN
Function / homology
Function and homology information


regulation of interferon-beta production / TRAF3 deficiency - HSE / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB 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 / Toll signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB 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 / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / protein K63-linked ubiquitination / positive regulation of type I interferon production / ubiquitin ligase complex / regulation of cytokine production / TICAM1-dependent activation of IRF3/IRF7 / tumor necrosis factor-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / 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 / defense response to virus / protein phosphatase binding / regulation of apoptotic process / endosome membrane / endosome / apoptotic process / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / mitochondrion / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
: / TNF receptor-associated factor 2/3/5, RING domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / : / TRAF/meprin, MATH domain ...: / TNF receptor-associated factor 2/3/5, RING domain / TNF receptor-associated factor 3 / TRAF3, MATH 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, 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 / SYNCHROTRON / Resolution: 2.8 Å
AuthorsNi, C.-Z. / Welsh, K. / Leo, E. / Chiou, C.-K. / Wu, H. / Reed, J.C. / Ely, K.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Molecular basis for CD40 signaling mediated by TRAF3.
Authors: Ni, C.Z. / Welsh, K. / Leo, E. / Chiou, C.K. / Wu, H. / Reed, J.C. / Ely, K.R.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: 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

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Assembly

Deposited unit
A: TNF RECEPTOR ASSOCIATED FACTOR 3
B: TNF RECEPTOR ASSOCIATED FACTOR 3


Theoretical massNumber of molelcules
Total (without water)51,7712
Polymers51,7712
Non-polymers00
Water0
1
A: TNF RECEPTOR ASSOCIATED FACTOR 3

A: TNF RECEPTOR ASSOCIATED FACTOR 3

A: TNF RECEPTOR ASSOCIATED FACTOR 3


Theoretical massNumber of molelcules
Total (without water)77,6573
Polymers77,6573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7160 Å2
ΔGint-53 kcal/mol
Surface area31460 Å2
MethodPISA
2
B: TNF RECEPTOR ASSOCIATED FACTOR 3

B: TNF RECEPTOR ASSOCIATED FACTOR 3

B: TNF RECEPTOR ASSOCIATED FACTOR 3


Theoretical massNumber of molelcules
Total (without water)77,6573
Polymers77,6573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area7220 Å2
ΔGint-50 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.530, 84.530, 319.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TNF RECEPTOR ASSOCIATED FACTOR 3 /


Mass: 25885.521 Da / Num. of mol.: 2 / Fragment: TRAF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / References: UniProt: Q13114

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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: 4.24 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: METHANOL, SODIUM CHLORIDE, TRIS BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 20, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 58040 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.9
Reflection shellResolution: 2.79→2.89 Å / Rmerge(I) obs: 0.24 / % possible all: 89.1
Reflection shell
*PLUS
% possible obs: 89.1 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.286 868 -RANDOM
Rwork0.224 ---
obs0.224 16837 88.2 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 0 0 3252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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