4DJ3 | pdb_00004dj3

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)
B	PARP	e4dj3B1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: PARP	ECOD (v294.1)
A	PAS_3	e4dj3A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: PAS_3	ECOD (v294.1)
A	Per3-like_PAS-A	e4dj3A2	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Per3-like_PAS-A	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	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	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	Period circadian protein homolog 3	protein binding binding kinase binding enzyme binding transcription factor binding transcription coregulator binding transcription corepressor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding protein binding binding kinase binding enzyme binding transcription factor binding transcription coregulator binding transcription corepressor binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding	rhythmic process circadian rhythm regulation of protein stability biological regulation regulation of biological quality protein stabilization response to light stimulus regulation of biological process entrainment of circadian clock response to stimulus response to external stimulus regulation of circadian rhythm photoperiodism response to radiation rhythmic process circadian rhythm regulation of protein stability biological regulation regulation of biological quality protein stabilization response to light stimulus regulation of biological process entrainment of circadian clock response to stimulus response to external stimulus regulation of circadian rhythm photoperiodism response to radiation response to abiotic stimulus entrainment of circadian clock by photoperiod circadian sleep/wake cycle, sleep multicellular organismal process circadian sleep/wake cycle rhythmic behavior regulation of circadian sleep/wake cycle regulation of behavior behavior circadian behavior regulation of multicellular organismal process sleep regulation of circadian sleep/wake cycle, sleep circadian sleep/wake cycle 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic 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 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 circadian regulation of gene expression	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	IPR000014	PAS domain	Domain
A, B	IPR057310	Period circadian protein homolog PER 1-3, bHLH-like domain	Domain
A, B	IPR048814	Period circadian protein homolog 1-3, PAS-A domain	Domain
A, B	IPR035965	PAS domain superfamily	Homologous Superfamily
A, B	IPR013655	PAS fold 3	Domain
A, B	IPR022728	Period circadian-like, C-terminal	Domain
A, B	IPR050760	Period circadian regulator	Family

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.