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- PDB-1l0a: DOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3 -

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Basic information

Entry
Database: PDB / ID: 1l0a
TitleDOWNSTREAM REGULATOR TANK BINDS TO THE CD40 RECOGNITION SITE ON TRAF3
Components
  • TNF receptor associated factor 3
  • TRAF family member-associated NF-kappa-b activator
KeywordsSIGNALING PROTEIN / CD40 / NF-kB signaling / TANK / TNF receptor / TRAF3
Function / homology
Function and homology information


regulation of interferon-beta production / positive regulation of protein deubiquitination / TRAF3 deficiency - HSE / positive regulation of ubiquitin-specific protease activity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex ...regulation of interferon-beta production / positive regulation of protein deubiquitination / TRAF3 deficiency - HSE / positive regulation of ubiquitin-specific protease activity / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Toll signaling pathway / CD40 receptor complex / regulation of defense response to virus / TRIF-dependent toll-like receptor signaling pathway / serine/threonine protein kinase complex / thioesterase binding / tumor necrosis factor receptor binding / deubiquitinase activator activity / regulation of canonical NF-kappaB signal transduction / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / molecular function inhibitor activity / toll-like receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / regulation of proteolysis / cellular response to interleukin-1 / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of type I interferon production / ubiquitin ligase complex / tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / signaling adaptor activity / 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 / regulation of cytokine production / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / cellular response to ionizing radiation / 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 / cellular response to tumor necrosis factor / TRAF3-dependent IRF activation pathway / protein phosphatase binding / regulation of apoptotic process / molecular adaptor activity / defense response to virus / cell surface receptor signaling pathway / endosome / endosome membrane / apoptotic process / ubiquitin protein ligase binding / DNA damage response / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / protein-containing complex / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
TRAF family member-associated NF-kappa-B activator / Tbk1/Ikki binding domain / TBD domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / TRAF-type zinc finger ...TRAF family member-associated NF-kappa-B activator / Tbk1/Ikki binding domain / TBD domain / TNF receptor-associated factor 3 / TRAF3, MATH domain / : / TNF receptor-associated factor 2/3/5, RING domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / 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 / TRAF family member-associated NF-kappa-B activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLi, C. / Ni, C.-Z. / Havert, M.L. / Cabezas, E. / He, J. / Kaiser, D. / Reed, J.C. / Satterthwait, A.C. / Cheng, G. / Ely, K.R.
CitationJournal: Structure / Year: 2002
Title: Downstream regulator TANK binds to the CD40 recognition site on TRAF3.
Authors: Li, C. / Ni, C.Z. / Havert, M.L. / Cabezas, E. / He, J. / Kaiser, D. / Reed, J.C. / Satterthwait, A.C. / Cheng, G. / Ely, K.R.
History
DepositionFeb 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator


Theoretical massNumber of molelcules
Total (without water)23,8872
Polymers23,8872
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-10 kcal/mol
Surface area11800 Å2
MethodPISA
2
A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator

A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator

A: TNF receptor associated factor 3
B: TRAF family member-associated NF-kappa-b activator


Theoretical massNumber of molelcules
Total (without water)71,6626
Polymers71,6626
Non-polymers00
Water1086
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 area13860 Å2
ΔGint-77 kcal/mol
Surface area28140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.000, 83.000, 76.700
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 / TRAF3 / CD40 receptor associated factor 1 / CRAF1 / CD40 binding protein / CD40BP


Mass: 21833.135 Da / Num. of mol.: 1 / Fragment: Residues 377-568 / Mutation: T195K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13114
#2: Protein/peptide TRAF family member-associated NF-kappa-b activator / TANK / TRAF-interacting protein / I-TRAF


Mass: 2054.343 Da / Num. of mol.: 1 / Fragment: Residues 178-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q92844
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100mM MES, 15% PEG1000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: unpublished data

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 7076 / Num. obs: 7042 / % possible obs: 99.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 5.5 % / % possible all: 100
Reflection
*PLUS
Num. obs: 7263 / Num. measured all: 38649 / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
CNSrefinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 386 -random
Rwork0.23 ---
all-7076 --
obs-7042 99.5 %-
Displacement parametersBiso mean: 37.3 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 28 1703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.42
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rfree: 0.295 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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