1U41

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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8054869	3000070	SCOP2B (2022-06-29)
D	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)
A	PF16179	e1u41A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16179	ECOD (1.6)
B	PF16179	e1u41B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16179	ECOD (1.6)
C	PF16179	e1u41C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16179	ECOD (1.6)
D	PF16179	e1u41D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF16179	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
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)

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	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding heat shock protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding heat shock protein binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein-containing complex binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-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	cellular response to nitrogen compound cellular response to stimulus response to organic substance cellular response to dsRNA response to stimulus cellular response to organic cyclic compound response to dsRNA response to nitrogen compound cellular response to chemical stimulus response to chemical cellular process cellular response to organic substance response to organic cyclic compound cellular response to interleukin-17 cellular response to nitrogen compound cellular response to stimulus response to organic substance cellular response to dsRNA response to stimulus cellular response to organic cyclic compound response to dsRNA response to nitrogen compound cellular response to chemical stimulus response to chemical cellular process cellular response to organic substance response to organic cyclic compound cellular response to interleukin-17 response to interleukin-17 response to cytokine cellular response to cytokine stimulus 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 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 regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process mammary gland morphogenesis mammary gland development gland development anatomical structure morphogenesis gland morphogenesis tissue remodeling mammary gland involution animal organ morphogenesis apoptotic process cell death programmed cell death biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus RNA metabolic process positive regulation of miRNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process regulation of miRNA metabolic process regulation of nucleobase-containing compound metabolic process miRNA metabolic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process nucleic acid metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process ncRNA metabolic process signaling non-canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction MAPK cascade negative regulation of biological process negative regulation of cellular metabolic process negative regulation of cellular process cytokine production regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cytokine production negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process response to peptide cellular response to peptide response to interleukin-6 cellular response to interleukin-6 JNK cascade negative regulation of RNA biosynthetic process DNA-templated transcription transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process positive regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of RNA biosynthetic process cellular response to interleukin-1 response to interleukin-1 organonitrogen compound biosynthetic process carbohydrate derivative metabolic process positive regulation of hyaluronan biosynthetic process glycosaminoglycan biosynthetic process carbohydrate biosynthetic process hyaluronan biosynthetic process positive regulation of carbohydrate metabolic process mucopolysaccharide metabolic process glycosaminoglycan metabolic process regulation of hyaluronan biosynthetic process regulation of polysaccharide metabolic process hyaluronan metabolic process polysaccharide metabolic process regulation of carbohydrate metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process organonitrogen compound metabolic process polysaccharide biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process regulation of carbohydrate biosynthetic process response to diterpene response to lipid cellular response to diterpene cellular response to lipid canonical NF-kappaB signal transduction immune response-regulating cell surface receptor signaling pathway 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 cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response 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 negative regulation of response to stimulus regulation of inflammatory response negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to biotic stimulus response to bacterium response to molecule of bacterial origin cellular response to tumor necrosis factor response to tumor necrosis factor regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of DNA-templated transcription initiation positive regulation of transcription initiation by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II 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 response to glucoside response to glycoside cellular response to glucoside regulation of interleukin-12 production negative regulation of interleukin-12 production interleukin-12 production 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 Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway regulation of cell communication positive regulation of signaling response to oxidative stress response to angiotensin response to organonitrogen compound response to peptide hormone cellular response to peptide hormone stimulus cellular response to angiotensin cellular response to organonitrogen compound response to hormone cellular response to hormone stimulus cellular response to carbohydrate stimulus response to carbohydrate cellular response to virus response to virus response to muscle stretch antibacterial innate immune response defense response to bacterium	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex intracellular organelle protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex transcription regulator complex intracellular organelle protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle 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	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	IPR033926	NFkappaB IPT domain	Domain
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	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A, B, C, D	IPR008967	p53-like transcription factor, DNA-binding 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	IPR000451	NF-kappa-B/Dorsal	Family
A, B, C, D	IPR047096	Nuclear factor NF-kappa-B p105 subunit, death domain	Domain
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 R01GM133198.