3JV6 | pdb_00003jv6

Crystal structure of the dimerization domains p52 and RelB

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)
F	d3jv6f_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3jv6d_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3jv6b_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3jv6e_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3jv6c_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3jv6a_	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain	automated matches	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)
F	SCOP2B Superfamily	E set domains	8100710	3000070	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	E set domains	8100710	3000070	SCOP2B (2022-06-29)
B	SCOP2 Family	NF-kappa-B/REL/DORSAL transcription factors, C-terminal domain-like	8100709	4007562	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	E set domains	8100710	3000070	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	E set domains	8054205	3000070	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	E set domains	8054205	3000070	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	E set domains	8054205	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)
F	FAD_binding_4	e3jv6F1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
D	FAD_binding_4	e3jv6D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
B	FAD_binding_4	e3jv6B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
E	FAD_binding_4	e3jv6E1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
C	FAD_binding_4	e3jv6C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)
A	FAD_binding_4	e3jv6A1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	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)
E	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)
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
B, D, F	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
A, C, E	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
B, D, F	Nuclear factor NF-kappa-B p100 subunit	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction developmental process multicellular organismal process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette cellular process signal transduction developmental process multicellular organismal process cellular developmental process follicular dendritic cell differentiation cell differentiation cell activation follicular dendritic cell activation immune system development multicellular organism development lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization response to peptide response to chemical response to cytokine non-canonical NF-kappaB signal transduction spleen development RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process rhythmic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains anatomical structure morphogenesis immune response anatomical structure formation involved in morphogenesis germinal center formation adaptive immune response positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound response to external stimulus response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen I-kappaB/NF-kappaB complex protein-containing complex Bcl3/NF-kappaB2 complex intracellular protein-containing complex
A, C, E	Transcription factor RelB	DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific DNA binding sequence-specific DNA binding binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific protein binding kinase binding enzyme binding protein kinase binding identical protein binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular response to stimulus response to stimulus signaling canonical NF-kappaB signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction developmental process multicellular organismal process myeloid leukocyte differentiation cellular developmental process myeloid dendritic cell activation hemopoiesis cell activation cell development mononuclear cell differentiation myeloid leukocyte activation leukocyte activation myeloid cell differentiation immune system process cell differentiation anatomical structure development myeloid dendritic cell differentiation dendritic cell differentiation leukocyte differentiation 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 response to peptide response to chemical response to cytokine negative regulation of type I interferon production cytokine production regulation of cytokine production regulation of multicellular organismal process regulation of interferon-beta production interferon-beta production type I interferon production negative regulation of cytokine production negative regulation of gene expression negative regulation of interferon-beta production negative regulation of multicellular organismal process regulation of type I interferon production non-canonical NF-kappaB signal transduction rhythmic process circadian regulation of gene expression circadian rhythm adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte activation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response T cell activation CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response alpha-beta T cell activation T cell differentiation lymphocyte activation involved in immune response T-helper cell differentiation T cell differentiation involved in immune response T-helper 1 type immune response adaptive immune response immune effector process T-helper 1 cell differentiation response to osmotic stress cellular response to chemical stress cellular response to osmotic stress cellular response to environmental stimulus cellular response to chemical stimulus cellular response to stress response to abiotic stimulus cellular response to abiotic stimulus inflammatory response antigen processing and presentation positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin chromosome protein-containing complex synapse cell junction transcription regulator complex transcription repressor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR030497	Nuclear factor NF-kappa-B, p100 subunit, RHD domain, N-terminal	Domain
B, D, F	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
B, D, F	IPR002909	IPT domain	Domain
B, D, F	IPR030492	Rel homology domain, conserved site	Conserved Site
B, D, F	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
B, D, F	IPR033926	NFkappaB IPT domain	Domain
B, D, F	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
B, D, F	IPR014756	Immunoglobulin E-set	Homologous Superfamily
B, D, F	IPR011539	Rel homology domain, DNA-binding domain	Domain
B, D, F	IPR002110	Ankyrin repeat	Repeat
B, D, F	IPR011029	Death-like domain superfamily	Homologous Superfamily
B, D, F	IPR000451	NF-kappa-B/Dorsal	Family
B, D, F	IPR032397	Rel homology dimerisation domain	Domain
B, D, F	IPR000488	Death domain	Domain
B, D, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E	IPR032399	RelB leucine zipper	Domain
A, C, E	IPR037059	Rel homology domain (RHD), DNA-binding domain superfamily	Homologous Superfamily
A, C, E	IPR002909	IPT domain	Domain
A, C, E	IPR030492	Rel homology domain, conserved site	Conserved Site
A, C, E	IPR033926	NFkappaB IPT domain	Domain
A, C, E	IPR008967	p53-like transcription factor, DNA-binding domain superfamily	Homologous Superfamily
A, C, E	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C, E	IPR011539	Rel homology domain, DNA-binding domain	Domain
A, C, E	IPR030496	Transcription factor RelB, RHD domain, N-terminal	Domain
A, C, E	IPR032400	RelB transactivation domain	Domain
A, C, E	IPR000451	NF-kappa-B/Dorsal	Family
A, C, E	IPR032397	Rel homology dimerisation domain	Domain
A, C, E	IPR013783	Immunoglobulin-like fold	Homologous Superfamily