3DO7,1SVC,1VKX


Conserved Protein Domain Family
RHD-n_NFkB

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cd07883: RHD-n_NFkB 
Click on image for an interactive view with Cn3D
N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-kappa B)
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 and B2 families of transcription factors, also referred to as class I members of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. Family members include NF-kappa B1 and NF-kappa B2. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form), while NF-kappa B2 is called p100 or p52 (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). p105 and p100 may also act as I-kappa Bs due to their C-terminal ankyrin repeats.
Statistics
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PSSM-Id: 143643
View PSSM: cd07883
Aligned: 7 rows
Threshold Bit Score: 354.862
Threshold Setting Gi: 254574803
Created: 31-Jul-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA binding
Conserved site includes 12 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:3DO7_B: Human NF-kappa B2 (p52)/RelB heterodimer binds DNA, only the NF-kappa B p100 and DNA strands are shown, contacts at 4A
    View structure with Cn3D
  • 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                       # ## ##  ###                                                      
3DO7_B          2 PYLVIVEQPKQRgFRFRYGCEgPSHGGLPGASse--kGRKTYPTVKICNYEgPAKIEVDLVTHSdpPRAHAHSLVGKQCS 79   human
1SVC_P         42 PYLQILEQPKQRgFRFRYVAEgPSHGGLPGASse--kNKKSYPQVKICNYVgPAKVIVQLVTNGknIHLHAHSLVGKHCE 119  human
1VKX_B          2 PYLQILEQPKQRgFRFRYVCEgPSHGGLPGASse--kNKKSYPQVKICNYVgPAKVIVQLVTNGknIHLHAHSLVGKHCE 79   house mouse
O96458         60 PHLKILEQPRQRgFRFRYGCEgPSHGGLPGQNsq--rGKRSFPSVEICNYKgSARIVVSLVTNEetPRPHAHSLVGKHCK 137  Strongylocent...
NP_001071772   24 PYLEIIENPKSRgFRFRYTCEgPSHGGIPGGSsd--kNKKTFPAVKICNYQgYARIVVQLVTNEenPRLHPHSLVGKQCQ 101  Ciona intesti...
ABU48530       48 PYLEILEQPKPRgFRFRYPSEgPSHGGLPGQFst--sKSKSYPSVQVNNYQgPCRIVVTLVTKDepYMLHAHSLTGKNAN 125  starlet sea a...
ABW76682       46 VRLEIVEQPKSRgFRFRYDCEgQSHGGLPGENseknrRQKTYPTVHLKGYRgRARVMVSLVTDSdpAMPHAHSIVGKNAI 125  Amphimedon qu...
Feature 1                                  # ##                                                   
3DO7_B         80 elGICAVSVGPk-DMTAQFNNLGVLHVTKKNMMGTMIQKLQRQrlrsrpq------------------------------ 128  human
1SVC_P        120 d-GICTVTAGPk-DMVVGFANLGILHVTKKKVFETLEARMTEAcirgynpgllvhpdla-----------------ylqa 180  human
1VKX_B         80 d-GVCTVTAGPk-DMVVGFANLGILHVTKKKVFETLEARMTEAcirgynpgllvhsdla-----------------ylqa 140  house mouse
O96458        138 d-GLCTVQVGPk-DMTASFPNLGILHVTRKDVVPTLKTRILAQhrlykdlinns-------------------------- 189  Strongylocent...
NP_001071772  102 n-GICTVQCGPk-DMTATFPNLGIQHVTKKNVATILEERYIAAemqlssindgfp------------------------- 154  Ciona intesti...
ABU48530      126 eeGVVTVQVGPdqHMTASFPNLGIQHVTKKNVVKVLMDRFIKWqtlqnatfaklsegikdgvdlslfgvntainsnklgf 205  starlet sea a...
ABW76682      126 d-GRCVVEIGPetDMYAQFTSLGILHVTKKKVPEVLTRRLLQQttprgqmvdqmevv----------------------d 182  Amphimedon qu...
Feature 1                                                                       #
3DO7_B        129 ------glteaeQRELEQEAKELKKVMDLSIVRLRFSAFLRDSDGSFSLPLKPVISQPIHDSK 185  human
1SVC_P        181 egggdrqlgdreKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSK 243  human
1VKX_B        141 egggdrqltdreKEIIRQAAVQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSK 203  house mouse
O96458        190 -tpgeshwtepsDAEIEKKAKEMAKDMDLSVVRLCFQTYLPDISGHFTRPLDPVISVPVFDSK 251  Strongylocentrotus purpuratus
NP_001071772  155 -qevqrnikdedRKRIAAKAQSEAKSIDLSVVRLMFIAYLPDSNGAFTIMLKPVISDAIFDSK 216  Ciona intestinalis
ABU48530      206 dknvalsvanqeAAKSREYAKQQAAAMDLSAVRLCFQAYLPDQDGNFTRPLKPVYSDAVLDSK 268  starlet sea anemone
ABW76682      183 vdmttaqltseeQDEIHQQAQTLAKSMNLSVVRLCFQAFLPDENGRYTIPIDPVFSNKVYDSK 245  Amphimedon queenslandica

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