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Yorodumi- PDB-2jvy: Solution Structure of the EDA-ID-related C417F mutant of human NE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jvy | ||||||
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Title | Solution Structure of the EDA-ID-related C417F mutant of human NEMO zinc finger | ||||||
Components | NF-kappa-B essential modulator | ||||||
Keywords | METAL BINDING PROTEIN / CCHC classical zinc finger / CCHF mutant zinc finger / EDA-ID C417F mutant of NEMO zinc finger / beta-beta-alpha fold / Coiled coil / Cytoplasm / Disease mutation / Ectodermal dysplasia / Host-virus interaction / Nucleus / Transcription / Transcription regulation | ||||||
Function / homology | Function and homology information IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / SLC15A4:TASL-dependent IRF5 activation / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / SLC15A4:TASL-dependent IRF5 activation / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / positive regulation of ubiquitin-dependent protein catabolic process / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / canonical NF-kappaB signal transduction / signaling adaptor activity / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / spindle pole / FCERI mediated NF-kB activation / Interleukin-1 signaling / Ovarian tumor domain proteases / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / defense response to bacterium / inflammatory response / immune response / protein heterodimerization activity / protein domain specific binding / innate immune response / ubiquitin protein ligase binding / DNA damage response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Cordier, F. / Vinolo, E. / Veron, M. / Delepierre, M. / Agou, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Solution structure of NEMO zinc finger and impact of an anhidrotic ectodermal dysplasia with immunodeficiency-related point mutation. Authors: Cordier, F. / Vinolo, E. / Veron, M. / Delepierre, M. / Agou, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jvy.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jvy.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jvy_validation.pdf.gz | 346.1 KB | Display | wwPDB validaton report |
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Full document | 2jvy_full_validation.pdf.gz | 390.1 KB | Display | |
Data in XML | 2jvy_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 2jvy_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/2jvy ftp://data.pdbj.org/pub/pdb/validation_reports/jv/2jvy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3281.732 Da / Num. of mol.: 1 / Fragment: zinc finger domain / Mutation: C417F / Source method: obtained synthetically Details: synthetic peptide, termini-blocked by N-acetyl and C-amide groups References: UniProt: Q9Y6K9 |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1 mM NEMO ZF-C417F, 2 mM ZnS04, 2 mM TCEP, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 6.6 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: The structure was determined using NOEs and dihedral angles data. Tetrahedral geometry of the zinc coordination was assumed involving only the thiol groups of C6 and C9 and the NE2 atom of ...Details: The structure was determined using NOEs and dihedral angles data. Tetrahedral geometry of the zinc coordination was assumed involving only the thiol groups of C6 and C9 and the NE2 atom of H22. Of the 200 calculated conformers, the 80 conformers with the lowest total energy were refined in water. The 10 refined conformers of lowest energy represent the final ensemble. | ||||||||||||||||||||||||||||||||
NMR constraints | Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 11 / Protein psi angle constraints total count: 0 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 |