1U41 | pdb_00001u41

Crystal structure of YLGV mutant of dimerisation domain of NF-kB p50 transcription factor

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)
C	d1u41c_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	p50 subunit of NF-kappa B transcription factor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d1u41d_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	p50 subunit of NF-kappa B transcription factor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1u41b_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	p50 subunit of NF-kappa B transcription factor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1u41a_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	p50 subunit of NF-kappa B transcription factor	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)
C	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Copper-bind	e1u41C1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
D	Copper-bind	e1u41D1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
B	Copper-bind	e1u41B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
A	Copper-bind	e1u41A1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
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
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Nuclear factor NF-kappa-B p105 subunit	protein binding binding heat shock protein binding sequence-specific DNA binding DNA binding nucleic acid binding protein-containing complex binding sequence-specific double-stranded DNA binding double-stranded DNA 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 protein binding binding heat shock protein binding sequence-specific DNA binding DNA binding nucleic acid binding protein-containing complex binding sequence-specific double-stranded DNA binding double-stranded DNA 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 transcription coregulator binding transcription coactivator binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding cis-regulatory region sequence-specific DNA binding identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity transcription coregulator activity RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding molecular sequestering activity protein sequestering activity cytoskeletal protein binding actinin binding	positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process regulation of transport biological regulation lipid localization lipid transport positive regulation of lipid localization establishment of localization positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization cholesterol transport cholesterol efflux developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor cellular process apoptotic process cell death programmed cell death regulation of cellular process RNA metabolic process positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process 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 cellular process primary metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of RNA metabolic process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus signaling non-canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction negative regulation of biological process negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process response to peptide response to interleukin-6 cellular response to interleukin-6 response to chemical response to cytokine cellular response to cytokine stimulus JNK cascade MAPK cascade signal transduction involved in regulation of gene expression negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process cellular response to interleukin-1 response to interleukin-1 glycosaminoglycan metabolic process regulation of hyaluronan biosynthetic process carbohydrate derivative metabolic process positive regulation of macromolecule biosynthetic process regulation of polysaccharide metabolic process hyaluronan metabolic process polysaccharide metabolic process positive regulation of hyaluronan biosynthetic process positive regulation of biosynthetic process glycosaminoglycan biosynthetic process regulation of carbohydrate metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process hyaluronan biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of developmental process cellular developmental process macrophage derived foam cell differentiation regulation of cell differentiation positive regulation of developmental process foam cell differentiation positive regulation of cell differentiation cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation cellular response to tumor necrosis factor response to tumor necrosis factor positive regulation of DNA-templated transcription regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of transcription initiation by RNA polymerase II positive regulation of transcription by RNA polymerase II DNA-templated transcription initiation positive regulation of DNA-templated transcription initiation positive regulation of RNA biosynthetic process regulation of transcription initiation by RNA polymerase II cellular response to chemical stimulus cellular response to nicotine response to nicotine response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus positive regulation of cell communication positive regulation of signal transduction regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of cell communication positive regulation of signaling response to oxidative stress cellular response to carbohydrate stimulus response to carbohydrate response to oxygen-containing compound cellular response to oxygen-containing compound biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont antibacterial innate immune response response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium innate immune response response to external biotic stimulus cellular response to nitrogen compound cellular response to dsRNA response to dsRNA response to nitrogen compound cellular response to interleukin-17 response to interleukin-17 positive regulation of response to external stimulus positive regulation of inflammatory response positive regulation of defense response positive regulation of gene expression mammary gland morphogenesis mammary gland development gland development anatomical structure morphogenesis gland morphogenesis tissue remodeling mammary gland involution animal organ morphogenesis cellular response to peptide cytokine-mediated signaling pathway tumor necrosis factor-mediated signaling pathway regulation of steroid biosynthetic process negative regulation of small molecule metabolic process steroid metabolic process regulation of lipid metabolic process vitamin biosynthetic process lipid biosynthetic process negative regulation of lipid biosynthetic process vitamin D biosynthetic process regulation of small molecule metabolic process small molecule metabolic process regulation of vitamin metabolic process steroid biosynthetic process negative regulation of steroid metabolic process small molecule biosynthetic process regulation of steroid metabolic process vitamin D metabolic process regulation of vitamin D biosynthetic process vitamin metabolic process negative regulation of vitamin metabolic process fat-soluble vitamin biosynthetic process negative regulation of steroid biosynthetic process regulation of lipid biosynthetic process negative regulation of vitamin D biosynthetic process negative regulation of lipid metabolic process lipid metabolic process response to diterpene response to lipid cellular response to lipid cellular response to diterpene canonical NF-kappaB signal transduction immune response-regulating cell surface receptor signaling pathway 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 immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response lipid storage regulation of lipid storage nutrient storage positive regulation of lipid storage cellular response to lipopolysaccharide cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to biotic stimulus response to molecule of bacterial origin response to glycoside cellular response to glucoside response to glucoside regulation of interleukin-12 production negative regulation of interleukin-12 production interleukin-12 production response to angiotensin response to peptide hormone cellular response to peptide hormone stimulus cellular response to angiotensin response to hormone cellular response to hormone stimulus cellular response to virus response to virus response to muscle stretch regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome I-kappaB/NF-kappaB complex intracellular protein-containing complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome I-kappaB/NF-kappaB complex intracellular protein-containing complex membrane-bounded organelle NF-kappaB p50/p65 complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle NF-kappaB complex mitochondrion membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR033926	NFkappaB IPT domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR011539	Rel homology domain, DNA-binding domain	Domain
A, B, C, D	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR047096	Nuclear factor NF-kappa-B p105 subunit, death domain	Domain
A, B, C, D	IPR030503	Nuclear factor NF-kappa-B, p105 subunit, Rel homology domain, N-terminal	Domain
A, B, C, D	IPR002909	IPT domain	Domain
A, B, C, D	IPR030492	Rel homology domain, conserved site	Conserved Site
A, B, C, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C, D	IPR002110	Ankyrin repeat	Repeat
A, B, C, D	IPR000488	Death domain	Domain
A, B, C, D	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR000451	NF-kappa-B/Dorsal	Family
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.