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- PDB-2jvy: Solution Structure of the EDA-ID-related C417F mutant of human NE... -

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Basic information

Entry
Database: PDB / ID: 2jvy
TitleSolution Structure of the EDA-ID-related C417F mutant of human NEMO zinc finger
ComponentsNF-kappa-B essential modulator
KeywordsMETAL 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) / 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 / positive regulation of ubiquitin-dependent protein catabolic process ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / 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 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / 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 / ubiquitin ligase complex / signaling adaptor activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / 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 / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / response to virus / NOD1/2 Signaling Pathway / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / T cell receptor signaling pathway / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / defense response to bacterium / immune response / inflammatory response / protein heterodimerization activity / protein domain specific binding / innate immune response / apoptotic process / DNA damage response / ubiquitin protein ligase binding / 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator
Similarity search - Domain/homology
NF-kappa-B essential modulator
Similarity search - Component
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCordier, F. / Vinolo, E. / Veron, M. / Delepierre, M. / Agou, F.
CitationJournal: 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
DepositionSep 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NF-kappa-B essential modulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3472
Polymers3,2821
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide NF-kappa-B essential modulator / NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / ...NEMO / NF-kappa-B essential modifier / Inhibitor of nuclear factor kappa-B kinase subunit gamma / IkB kinase subunit gamma / I-kappa-B kinase gamma / IKK-gamma / IKKG / IkB kinase-associated protein 1 / IKKAP1 / FIP-3


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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D purged-COSY

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Sample preparation

DetailsContents: 1 mM NEMO ZF-C417F, 2 mM ZnS04, 2 mM TCEP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMNEMO ZF-C417F1
2 mMZnS041
2 mMTCEP1
Sample conditionsIonic strength: 0 / pH: 6.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2.2Delaglio, F. et al.processing
NMRView5.03Johnson, B.A. et al.data analysis
NMRView5.03Johnson, B.A. et al.peak picking
NMRView5.03Johnson, B.A. et al.chemical shift assignment
ARIA1.2Linge, J.P. et al.structure solution
ARIA1.2Linge, J.P. et al.refinement
RefinementMethod: 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 constraintsProtein 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 representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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