4DJ2 | pdb_00004dj2

Unwinding the Differences of the Mammalian PERIOD Clock Proteins from Crystal Structure to Cellular Function

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	PAS_11	e4dj2D2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
D	KOG3753	e4dj2D1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: KOG3753	ECOD (1.6)
C	PAS_11	e4dj2C1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
C	KOG3753	e4dj2C2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: KOG3753	ECOD (1.6)
B	PAS_11	e4dj2B9	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
B	KOG3753	e4dj2B10	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: KOG3753	ECOD (1.6)
A	PAS_11	e4dj2A1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: PAS_11	ECOD (1.6)
A	KOG3753	e4dj2A2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: KOG3753	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
C	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
B	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)
A	3.30.450.20	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	PAS domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF21353	Period circadian protein homolog 3-like, PAS-A domain (Per3-like_PAS-A)	Period circadian protein homolog 3-like, PAS-A domain	This domain is found in Period circadian protein homolog 3 from Mus musculus (Per3) and similar proteins predominantly found in vertebrates. Per3 is involved in the day-time dependent (circadian) regulation of many physiological, behavioural, and bio ...	This domain is found in Period circadian protein homolog 3 from Mus musculus (Per3) and similar proteins predominantly found in vertebrates. Per3 is involved in the day-time dependent (circadian) regulation of many physiological, behavioural, and biochemical processes. This entry represents the first PAS domain (PAS-A) present in this protein. This domain shows a five-stranded antiparallel beta- sheet covered on one face by alpha-helices [1-4].	Domain
A, B, C, D	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, B, C, D	Period circadian protein homolog 1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding kinase binding enzyme binding chromatin binding chromatin DNA binding transcription factor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding kinase binding enzyme binding chromatin binding chromatin DNA binding transcription factor binding DNA-binding transcription factor binding E-box binding 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 ubiquitin protein ligase binding ubiquitin-like protein ligase 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 rhythmic process circadian rhythm regulation of circadian rhythm cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction intracellular receptor signaling pathway response to lipid hormone-mediated signaling pathway cellular response to endogenous stimulus negative regulation of intracellular steroid hormone receptor signaling pathway response to hormone response to steroid hormone regulation of intracellular steroid hormone receptor signaling pathway nuclear receptor-mediated steroid hormone signaling pathway cellular response to steroid hormone stimulus steroid hormone receptor signaling pathway cellular response to hormone stimulus response to endogenous stimulus nuclear receptor-mediated corticosteroid signaling pathway cellular response to chemical stimulus response to chemical cellular response to lipid negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated signaling pathway regulation of nuclear receptor-mediated glucocorticoid signaling pathway nuclear receptor-mediated glucocorticoid signaling pathway post-transcriptional regulation of gene expression circadian regulation of gene expression negative regulation of JNK cascade JNK cascade regulation of JNK cascade regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade multicellular organismal process hair cycle molting cycle regulation of hair cycle regulation of multicellular organismal process response to light stimulus entrainment of circadian clock response to external stimulus photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod p38MAPK cascade regulation of p38MAPK cascade regulation of cytokine production involved in inflammatory response response to stress cytokine production regulation of cytokine production production of molecular mediator involved in inflammatory response defense response cytokine production involved in inflammatory response inflammatory response response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of localization transport regulation of transport regulation of monoatomic ion transport regulation of sodium ion transport establishment of localization metal ion transport localization monoatomic ion transport regulation of metal ion transport monoatomic cation transport sodium ion transport cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013655	PAS fold-3	Domain
A, B, C, D	IPR022728	Period circadian-like, C-terminal	Domain
A, B, C, D	IPR050760	Period circadian regulator	Family
A, B, C, D	IPR000014	PAS domain	Domain
A, B, C, D	IPR048814	Period circadian protein homolog 1-3, PAS-A domain	Domain
A, B, C, D	IPR035965	PAS domain superfamily	Homologous Superfamily

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.