5SY5

Crystal Structure of the Heterodimeric NPAS1-ARNT Complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HLH	e5sy5A2	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
A	PAS_11	e5sy5A3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
A	PAS_11_1	e5sy5A1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11_1	ECOD (1.6)
C	HLH	e5sy5C1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
C	PAS_11	e5sy5C3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
C	PAS_11_1	e5sy5C2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11_1	ECOD (1.6)
E	HLH	e5sy5E1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
E	PAS_11	e5sy5E2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
E	PAS_11_1	e5sy5E3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11_1	ECOD (1.6)
B	HLH	e5sy5B2	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
B	PAS_11	e5sy5B1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
B	PAS_11_1	e5sy5B3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11_1	ECOD (1.6)
D	HLH	e5sy5D2	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
D	PAS_11	e5sy5D1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
D	PAS_11_1	e5sy5D3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11_1	ECOD (1.6)
F	HLH	e5sy5F1	A: alpha duplicates or obligate multimers	X: HLH-like	H: HLH, helix-loop-helix DNA-binding domain (From Topology)	T: HLH, helix-loop-helix DNA-binding domain	F: HLH	ECOD (1.6)
F	PAS_11	e5sy5F3	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
F	PAS_11_1	e5sy5F2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF00989	PAS fold (PAS)	PAS fold	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (M ...	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
A, C, E	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain	-	Domain
A, C, E	PF14598	PAS domain (PAS_11)	PAS domain	This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6) [1].	Domain
B, D, F	PF00010	Helix-loop-helix DNA-binding domain (HLH)	Helix-loop-helix DNA-binding domain	-	Domain
B, D, F	PF08447	PAS fold (PAS_3)	PAS fold	The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E	Aryl hydrocarbon receptor nuclear translocator	transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding DNA binding sequence-specific DNA 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 organic cyclic compound binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding binding DNA-binding transcription factor binding DNA binding sequence-specific DNA 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 organic cyclic compound binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding protein heterodimerization activity protein dimerization activity transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific identical protein binding protein homodimerization activity protein-containing complex binding nuclear receptor activity molecular transducer activity ligand-activated transcription factor activity signaling receptor activity signaling receptor binding aryl hydrocarbon receptor binding	developmental process cellular developmental process cell differentiation cellular process regulation of protein sumoylation regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process regulation of nitrogen compound metabolic process positive regulation of metabolic process positive regulation of protein modification process developmental process cellular developmental process cell differentiation cellular process regulation of protein sumoylation regulation of protein modification process positive regulation of protein metabolic process peptidyl-lysine modification positive regulation of biological process positive regulation of post-translational protein modification regulation of primary metabolic process regulation of nitrogen compound metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process peptidyl-amino acid modification nitrogen compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of protein modification by small protein conjugation or removal regulation of biological process organonitrogen compound metabolic process regulation of post-translational protein modification regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of nitrogen compound metabolic process protein sumoylation macromolecule modification metabolic process macromolecule metabolic process positive regulation of protein sumoylation post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal multicellular organismal process regulation of cellular process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of multicellular organismal process positive regulation of cellular process regulation of vascular endothelial growth factor production regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression vascular endothelial growth factor production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of defense response response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus negative regulation of biological process 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 hormone biosynthetic process regulation of hormone metabolic process regulation of biological quality hormone biosynthetic process positive regulation of hormone metabolic process regulation of hormone levels hormone metabolic process positive regulation of hormone biosynthetic process placenta development chordate embryonic development animal organ development embryo development in utero embryonic development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching anatomical structure development embryonic organ development response to chemical response to toxic substance cellular response to stimulus response to oxidative stress cellular response to chemical stimulus cellular response to stress cellular response to oxidative stress cellular response to chemical stress response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process cellular nitrogen compound metabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process nucleic acid metabolic process positive regulation of RNA biosynthetic process cellular aromatic compound metabolic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen aryl hydrocarbon receptor complex receptor complex nuclear aryl hydrocarbon receptor complex intracellular protein-containing complex nuclear body
B, D, F	Neuronal PAS domain-containing protein 1	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein heterodimerization activity protein binding binding protein dimerization activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity protein heterodimerization activity protein binding binding protein dimerization activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding	regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of cellular process negative regulation of biological process negative regulation of nitrogen compound metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process regulation of nitrogen compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process aromatic compound biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic 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 biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process nitrogen compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process cellular aromatic compound metabolic process startle response multicellular organismal process system process response to stimulus nervous system process neuromuscular process response to external stimulus maternal behavior behavior parental behavior reproductive process multicellular organismal reproductive process reproductive behavior transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR013767	PAS fold	Domain
A, C, E	IPR001067	Nuclear translocator	Family
A, C, E	IPR000014	PAS domain	Domain
A, C, E	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
A, C, E	IPR035965	PAS domain superfamily	Homologous Superfamily
A, C, E	IPR001610	PAC motif	Repeat
A, C, E	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily
B, D, F	IPR013767	PAS fold	Domain
B, D, F	IPR000014	PAS domain	Domain
B, D, F	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain	Domain
B, D, F	IPR035965	PAS domain superfamily	Homologous Superfamily
B, D, F	IPR013655	PAS fold-3	Domain
B, D, F	IPR036638	Helix-loop-helix DNA-binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.