2RAM

A NOVEL DNA RECOGNITION MODE BY NF-KB P65 HOMODIMER

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth B]	d2ramb1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	p65 subunit of NF-kappa B (NFKB), dimerization domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d2ramb2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	Rel/Dorsal transcription factors, DNA-binding domain	p65 subunit of NF-kappa B (NFKB), N-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth A]	d2rama1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	p65 subunit of NF-kappa B (NFKB), dimerization domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth A]	d2rama2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	p53-like transcription factors	Rel/Dorsal transcription factors, DNA-binding domain	p65 subunit of NF-kappa B (NFKB), N-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	p53-like transcription factors	8040233	3000758	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	E set domains	8054875	3000070	SCOP2B (2022-06-29)
C [auth A]	SCOP2 Family	Rel/Dorsal transcription factors, DNA-binding domain	8027854	4001849	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Family	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain-like	8054874	4007562	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	p53-like transcription factors	8040233	3000758	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	E set domains	8054875	3000070	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth B]	RHD_dimer	e2ramB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RHD_dimer	ECOD (1.6)
D [auth B]	RHD_DNA_bind	e2ramB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: RHD_DNA_bind	ECOD (1.6)
C [auth A]	RHD_dimer	e2ramA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RHD_dimer	ECOD (1.6)
C [auth A]	RHD_DNA_bind	e2ramA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: RHD_DNA_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	2.60.40.340	Mainly Beta	Sandwich	Immunoglobulin-like	Rel homology domain (RHD), DNA-binding domain	CATH (4.3.0)
D [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	2.60.40.340	Mainly Beta	Sandwich	Immunoglobulin-like	Rel homology domain (RHD), DNA-binding domain	CATH (4.3.0)
C [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF16179	Rel homology dimerisation domain (RHD_dimer)	Rel homology dimerisation domain	The Rel homology domain (RHD) is composed of two structural domains, an N-terminal DNA_binding domain (Pfam:PF00554) and a C-terminal dimerisation domain. This is the dimerisation domain [1].	Domain
C [auth A], D [auth B]	PF00554	Rel homology DNA-binding domain (RHD_DNA_bind)	Rel homology DNA-binding domain	Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal DNA-binding domain that is similar to that found in P53. The C-terminal domain has an immu ...	Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal DNA-binding domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See Pfam:PF16179) that functions as a dimerisation domain [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	DNA (5'-D(CPGPGPCPTPGPGPAPAPAPTP(5IU)P(5IU)PCPCPAPGPCPCPG)-3')	-	-	-
C [auth A], D [auth B]	PROTEIN (TRANSCRIPTION FACTOR NF-KB P65)	histone deacetylase binding protein binding binding enzyme binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding double-stranded DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding histone deacetylase binding protein binding binding enzyme binding sequence-specific DNA binding DNA binding organic cyclic compound binding nucleic acid binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding double-stranded DNA binding core promoter sequence-specific DNA binding RNA polymerase II core promoter sequence-specific DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding general transcription initiation factor binding ankyrin repeat binding protein domain specific binding ion binding anion binding phosphate ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity kinase binding protein kinase binding transcription coregulator binding transcription coactivator binding chromatin binding chromatin DNA binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding NF-kappaB binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding cytoskeletal protein binding actinin binding peptide binding	response to stimulus response to chemical response to xenobiotic stimulus response to tumor cell defense response response to stress defense response to tumor cell response to biotic stimulus response to ischemia cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation response to stimulus response to chemical response to xenobiotic stimulus response to tumor cell defense response response to stress defense response to tumor cell response to biotic stimulus response to ischemia cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation cell-cell signaling postsynaptic signal transduction cell communication synaptic signaling cellular process postsynapse to nucleus signaling pathway signal transduction cellular response to growth factor stimulus cell surface receptor signaling pathway response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway vascular endothelial growth factor signaling pathway cellular response to endogenous stimulus cellular response to vascular endothelial growth factor stimulus response to growth factor enzyme-linked receptor protein signaling pathway catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process non-canonical NF-kappaB signal transduction intracellular signal transduction intracellular signaling cassette positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA-templated transcription positive regulation of metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process regulation of cellular metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular biosynthetic process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of miRNA transcription positive regulation of cellular metabolic process positive regulation of miRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process miRNA transcription positive regulation of biosynthetic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process regulation of miRNA transcription response to nutrient levels response to cobalamin response to nutrient response to oxygen-containing compound response to nitrogen compound response to vitamin response to organic cyclic compound multicellular organismal process positive regulation of interleukin-8 production cytokine production regulation of cytokine production regulation of multicellular organismal process interleukin-8 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production regulation of interleukin-8 production positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway regulation of antigen receptor-mediated signaling pathway regulation of signal transduction positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process regulation of signaling immune response-activating cell surface receptor signaling pathway immune response regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling response to peptide response to interleukin-6 cellular response to interleukin-6 response to cytokine cellular response to cytokine stimulus biological process involved in interspecies interaction between organisms cellular response to lipoteichoic acid response to other organism response to lipoteichoic acid response to external stimulus cellular response to molecule of bacterial origin cellular response to oxygen-containing compound cellular response to biotic stimulus cellular response to chemical stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin negative regulation of signaling negative regulation of biological process regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process apoptotic process programmed cell death regulation of apoptotic signaling pathway response to organophosphorus response to purine-containing compound response to cAMP negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process cellular aldehyde metabolic process acetaldehyde metabolic process cellular component organization chromatin organization cellular component organization or biogenesis G protein-coupled receptor signaling pathway neuropeptide signaling pathway positive regulation of canonical NF-kappaB signal transduction regulation of intracellular signal transduction positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction developmental process epithelium development epidermis development molting cycle process hair cycle animal organ development tissue development skin development skin epidermis development hair follicle development molting cycle anatomical structure development hair cycle process regulation of interleukin-12 production interleukin-12 production positive regulation of interleukin-12 production cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of miRNA transcription negative regulation of miRNA metabolic process cellular response to tumor necrosis factor response to tumor necrosis factor regulation of amide metabolic process amyloid precursor protein catabolic process positive regulation of protein metabolic process regulation of amyloid-beta formation positive regulation of amyloid-beta formation regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process amide metabolic process amyloid precursor protein metabolic process amyloid-beta formation regulation of protein metabolic process positive regulation of amide metabolic process positive regulation of amyloid precursor protein catabolic process cellular response to nicotine response to nicotine response to hormone response to peptide hormone response to insulin regulation of non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction cytokine-mediated signaling pathway cellular response to interleukin-1 interleukin-1-mediated signaling pathway response to interleukin-1 inflammatory response regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis regulation of anatomical structure morphogenesis system development blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process negative regulation of post-translational protein modification regulation of protein sumoylation regulation of protein modification process peptidyl-lysine modification peptidyl-amino acid modification negative regulation of protein modification process protein modification process regulation of protein modification by small protein conjugation or removal negative regulation of protein sumoylation negative regulation of protein metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein sumoylation macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte cell-cell adhesion positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion leukocyte adhesion to vascular endothelial cell regulation of leukocyte cell-cell adhesion regulation of cell-cell adhesion response to ketone response to lipid response to steroid hormone response to progesterone response to light stimulus response to radiation response to abiotic stimulus response to UV response to UV-B defense response to symbiont defense response to other organism innate immune response interleukin-1 production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production positive regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production cellular response to nitrogen compound insulin receptor signaling pathway regulation of cellular response to insulin stimulus cellular response to hormone stimulus regulation of insulin receptor signaling pathway cellular response to peptide hormone stimulus negative regulation of cellular response to insulin stimulus negative regulation of insulin receptor signaling pathway cellular response to insulin stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway innate immune response-activating signaling pathway regulation of innate immune response positive regulation of defense response activation of innate immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus intracellular receptor signaling pathway positive regulation of response to external stimulus regulation of response to stress nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway nucleotide-binding oligomerization domain containing 2 signaling pathway positive regulation of innate immune response positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity positive regulation of molecular function regulation of molecular function regulation of DNA-binding transcription factor activity tumor necrosis factor-mediated signaling pathway negative regulation of catabolic process regulation of catabolic process negative regulation of protein catabolic process regulation of protein catabolic process positive regulation of transcription by RNA polymerase II hepaticobiliary system development gland development liver development response to acid chemical response to amino acid animal organ morphogenesis cell surface toll-like receptor signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway toll-like receptor 4 signaling pathway cellular response to peptidoglycan response to peptidoglycan regulation of vascular endothelial growth factor production vascular endothelial growth factor production positive regulation of vascular endothelial growth factor production interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of nervous system development cellular developmental process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis gliogenesis positive regulation of cell differentiation cell differentiation positive regulation of neurogenesis Schwann cell differentiation positive regulation of Schwann cell differentiation positive regulation of cell development regulation of glial cell differentiation peripheral nervous system development nervous system development positive regulation of glial cell differentiation regulation of Schwann cell differentiation glial cell differentiation cellular response to lipopolysaccharide response to lipopolysaccharide cellular response to lipid regulation of cartilage development regulation of chondrocyte differentiation connective tissue development positive regulation of chondrocyte differentiation skeletal system development chondrocyte differentiation positive regulation of cartilage development cartilage development cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress hormone-mediated signaling pathway prolactin signaling pathway regulation of inflammatory response response to muramyl dipeptide response to hepatocyte growth factor cellular response to hepatocyte growth factor stimulus negative regulation of intracellular signal transduction negative regulation of non-canonical NF-kappaB signal transduction response to angiotensin cellular response to angiotensin response to mechanical stimulus response to muscle stretch	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle NF-kappaB complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular non-membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle NF-kappaB complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle synapse cell junction glutamatergic synapse NF-kappaB p50/p65 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR033926	NFkappaB IPT domain	Domain
C [auth A], D [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth A], D [auth B]	IPR011539	Rel homology domain, DNA-binding domain	Domain
C [auth A], D [auth B]	IPR030495	Transcription factor p65, RHD domain, N-terminal	Domain
C [auth A], D [auth B]	IPR002909	IPT domain	Domain
C [auth A], D [auth B]	IPR030492	Rel homology domain, conserved site	Conserved Site
C [auth A], D [auth B]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C [auth A], D [auth B]	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR000451	NF-kappa-B/Dorsal	Family
C [auth A], D [auth B]	IPR032397	Rel homology dimerisation domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.