6NOD | pdb_00006nod

Crystal structure of C. elegans PUF-8 in complex with RNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pumilio repeat	8085030	4003086	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8085031	3000116	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	ARM repeat-like	8085031	3000116	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8085031	3000116	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	ubiquitin	e6nodA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: ubiquitin	ECOD (v294.1)
B	ubiquitin	e6nodB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: ubiquitin	ECOD (v294.1)
C	ubiquitin	e6nodC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: ubiquitin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (utative)
B	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (utative)
C	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00806	Pumilio-family RNA binding repeat (PUF)	Pumilio-family RNA binding repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	RNA (5'-R(PUPGPUPAPUPAPUPA)-3')	-	-	-
A, B, C	PUF (Pumilio/FBF) domain-containing	mRNA 3'-UTR binding RNA binding binding nucleic acid binding mRNA binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of cellular process response to stimulus developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation regulation of MAPK cascade negative regulation of signal transduction regulation of response to stimulus MAPK cascade regulation of cell communication negative regulation of MAPK cascade regulation of biosynthetic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process protein metabolic process regulation of metabolic process organelle fission meiotic cell cycle male meiotic nuclear division meiotic cell cycle process cellular component organization nuclear division organelle organization meiotic nuclear division cellular component organization or biogenesis cell cycle cell cycle process	intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle intracellular anatomical structure P granule cytoplasmic ribonucleoprotein granule germ plasm intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle pole plasm membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B, C	IPR033712	Pumilio, RNA binding domain	Domain
A, B, C	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B, C	IPR001313	Pumilio RNA-binding repeat	Repeat
A, B, C	IPR033133	Pumilio homology 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.