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
View PSSM: cd07935
Aligned: 5 rows
Threshold Bit Score: 394.26
Threshold Setting Gi: 125968525
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 PYLQILEQPKQRgFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGk-nIHLHAHSLVGKHCED 80   house mouse
NP_001087808  41 PYIEITEQPKQRgFRFRYVCEGPSHGGLPGASSEKNRKSYPQIKIHNYVGQVKVVVQLITNSk-dIRLHAHSLVGKNCED 119  African clawed...
Q04861        47 PYLQIIEQPKQRgFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGk-yRHLHAHSLVGKFCED 125  chicken
ABN58794      40 PFLQIVEQPKQRgFRFRYGCEGPSHGGLPGASSEKNRKTYPTVKISNYQGPSRVVVQLVTALtplPQLHAHSLVGKQCDK 119  Chinese perch
1SVC_P        42 PYLQILEQPKQRgFRFRYVAEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGk-nIHLHAHSLVGKHCED 120  human
Feature 1                              # ##                                                      
1VKX_B        81 GVCTVTAGPkDMVVGFANLGILHVTKKKVFETLEARMTEACIRGyNPGLLVHSDLAYlqaegggdRQLTDREKEIIRQAA 160  house mouse
NP_001087808 120 GICSLTVGPkDTIVGFPNLGILHVTKKKVIEILEARMTDAFKKGhNAALLVHPELNYtns---edRPLNEREKEIIRQAA 196  African clawed...
Q04861       126 GVCTVNAGPkDMVVGFANLGILHVTKKKVFETLETRMIDACKKGyNPGLLVHPELGYlqaegcgdRQLTEREREIIRQAA 205  chicken
ABN58794     120 GICIADLQPkDSNISFPDLGILHVTKKNVAKTLEERMIEAYRMGyNCGVSIHPEIDAvqgevrvpRDLTEHQRSVISSVA 199  Chinese perch
1SVC_P       121 GICTVTAGPkDMVVGFANLGILHVTKKKVFETLEARMTEACIRGyNPGLLVHPDLAYlqaegggdRQLGDREKELIRQAA 200  human
Feature 1                                                  #
1VKX_B       161 VQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSK 203  house mouse
NP_001087808 197 TQQSKDIDLSVVRLMFTAFLLDSEGRFTRSLEPVLSVPIFDSK 239  African clawed frog
Q04861       206 VQQTKEMDLSVVRLMFTAFLPDSNGGFTRRLDPVISDAIYDSK 248  chicken
ABN58794     200 ALQAKEMDLSVVRLMFTAFLPDSDGGFSRRLEPVVSEPIYDSK 242  Chinese perch
1SVC_P       201 LQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSK 243  human

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