1VKX,1SVC


Conserved Protein Domain Family
RHD-n_NFkB1

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cd07935: RHD-n_NFkB1 
Click on image for an interactive view with Cn3D
N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1)
Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B1 family of transcription factors, a class I member of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and REL). NF-kappa B1 is involved in the canonical NF-kappa B signaling pathway which is activated by many agonists and is essential in immune and inflammatory responses, as well as cell survival. p105 is involved in its own specific NF-kappa B signaling pathway which is also implicated in immune and inflammatory responses. p105 may also act as an I-kappa B due to its C-terminal ankyrin repeats. It is also involved in mitogen-activated protein kinase (MAPK) signaling as its degradation leads to the activation of TPL-2, a MAPK kinase kinase which activates ERK pathways.
Statistics
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PSSM-Id: 143651
Aligned: 5 rows
Threshold Bit Score: 394.26
Created: 15-Sep-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding site [nucleic acid binding site]
Evidence:
  • Structure:1SVC: Human NF-kappa B1 (p50) homodimer binds DNA, only a single monomer and DNA strand are shown, contacts at 4A
    View structure with Cn3D
  • Citation:PMID 7830764
  • Structure:1VKX: Mus musculus NF-kappa B1 (p50) and RelA (p65) heterodimer binds DNA, contacts at 4A
    View structure with Cn3D
  • Citation:PMID 9450761

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:

Feature 1                          # ## ##  ####                                                 
1VKX_B         2 PYLQILEQPKQR.[1].FRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNG.[2].IHLHAHSLV 74   house mouse
NP_001087808  41 PYIEITEQPKQR.[1].FRFRYVCEGPSHGGLPGASSEKNRKSYPQIKIHNYVGQVKVVVQLITNS.[2].IRLHAHSLV 113  African clawed frog
Q04861        47 PYLQIIEQPKQR.[1].FRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNG.[2].RHLHAHSLV 119  chicken
ABN58794      40 PFLQIVEQPKQR.[1].FRFRYGCEGPSHGGLPGASSEKNRKTYPTVKISNYQGPSRVVVQLVTAL.[3].PQLHAHSLV 113  Chinese perch
1SVC_P        42 PYLQILEQPKQR.[1].FRFRYVAEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNG.[2].IHLHAHSLV 114  human

Feature 1                                        # ##                                            
1VKX_B        75 GKHCEDGVCTVTAGP.[1].DMVVGFANLGILHVTKKKVFETLEARMTEACIRG.[1].NPGLLVHSDLAY.[8].RQLT 149  house mouse
NP_001087808 114 GKNCEDGICSLTVGP.[1].DTIVGFPNLGILHVTKKKVIEILEARMTDAFKKG.[1].NAALLVHPELNY.[5].RPLN 185  African clawed frog
Q04861       120 GKFCEDGVCTVNAGP.[1].DMVVGFANLGILHVTKKKVFETLETRMIDACKKG.[1].NPGLLVHPELGY.[8].RQLT 194  chicken
ABN58794     114 GKQCDKGICIADLQP.[1].DSNISFPDLGILHVTKKNVAKTLEERMIEAYRMG.[1].NCGVSIHPEIDA.[8].RDLT 188  Chinese perch
1SVC_P       115 GKHCEDGICTVTAGP.[1].DMVVGFANLGILHVTKKKVFETLEARMTEACIRG.[1].NPGLLVHPDLAY.[8].RQLG 189  human

Feature 1                                                             #
1VKX_B       150 DREKEIIRQAAVQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSK 203  house mouse
NP_001087808 186 EREKEIIRQAATQQSKDIDLSVVRLMFTAFLLDSEGRFTRSLEPVLSVPIFDSK 239  African clawed frog
Q04861       195 EREREIIRQAAVQQTKEMDLSVVRLMFTAFLPDSNGGFTRRLDPVISDAIYDSK 248  chicken
ABN58794     189 EHQRSVISSVAALQAKEMDLSVVRLMFTAFLPDSDGGFSRRLEPVVSEPIYDSK 242  Chinese perch
1SVC_P       190 DREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSK 243  human

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