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- PDB-2dbf: Solution structure of the Death domain in human Nuclear factor NF... -

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Basic information

Entry
Database: PDB / ID: 2dbf
TitleSolution structure of the Death domain in human Nuclear factor NF-kappa-B p105 subunit
ComponentsNuclear factor NF-kappa-B p105 subunit
KeywordsSIGNALING PROTEIN / apoptosis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / positive regulation of hyaluronan biosynthetic process / mammary gland involution / antibacterial innate immune response / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID ...: / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / positive regulation of hyaluronan biosynthetic process / mammary gland involution / antibacterial innate immune response / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / CLEC7A/inflammasome pathway / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / cellular response to interleukin-6 / cellular response to dsRNA / actinin binding / positive regulation of macrophage derived foam cell differentiation / signal transduction involved in regulation of gene expression / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / Regulation of NFE2L2 gene expression / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / cellular response to interleukin-1 / cellular response to angiotensin / positive regulation of cholesterol efflux / canonical NF-kappaB signal transduction / positive regulation of transcription initiation by RNA polymerase II / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / negative regulation of cytokine production involved in inflammatory response / CD209 (DC-SIGN) signaling / protein sequestering activity / NF-kB is activated and signals survival / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / transcription coregulator activity / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / cellular response to virus / PKMTs methylate histone lysines / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / CLEC7A (Dectin-1) signaling / negative regulation of inflammatory response / cellular response to nicotine / FCERI mediated NF-kB activation / specific granule lumen / Interleukin-1 signaling / HCMV Early Events / cellular response to mechanical stimulus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / Senescence-Associated Secretory Phenotype (SASP) / secretory granule lumen / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / apoptotic process / chromatin binding / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p105 subunit / : / Death Domain, Fas / Death Domain, Fas / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain ...Nuclear factor NF-kappa-B, p105 subunit / : / Death Domain, Fas / Death Domain, Fas / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Inoue, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the Death domain in human Nuclear factor NF-kappa-B p105 subunit
Authors: Saito, K. / Inoue, M. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)10,6221
Polymers10,6221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear factor NF-kappa-B p105 subunit / KBF1 / DNA-binding factor KBF1 / EBP- 1


Mass: 10621.934 Da / Num. of mol.: 1 / Fragment: DEATH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: PR1117_G03 / Plasmid: P050613-15 / References: UniProt: P19838

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM protein; 20mM d-tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
NMRPipe2002DELAGLIO, F.processing
NMRView5JOHNSON, B.A.data analysis
CNS1.1BRUNGER, A.T.structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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