7NDJ | pdb_00007ndj

Crystal structure of ZC3H12C PIN-CCCH Zn Finger domain with RNA heptamer

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)
B	SCOP2 Family	Zc3h12a NYN domain-like	8106301	4005493	SCOP2 (2022-06-29)
B	SCOP2 Family	CCCH zinc finger	8106383	4003893	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PIN domain-like	8106302	3001041	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CCCH zinc finger-like	8106384	3001741	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	PIN domain-like	8106302	3001041	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)
B	P-II	e7ndjB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: P-II	ECOD (v294.1)
A	14-3-3	e7ndjA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: 14-3-3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.11980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
A	3.40.50.11980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11977	Zc3h12a-like Ribonuclease NYN domain (RNase_Zc3h12a)	Zc3h12a-like Ribonuclease NYN domain	This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [1]. It has been suggested that this domain belongs to the PIN domain superfamily [1]. This domain has also be ...	This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [1]. It has been suggested that this domain belongs to the PIN domain superfamily [1]. This domain has also been identified as part of the NYN domain family [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	RNA (5'-R(UPUPAPUPUPAP*U)-3')	-	-	-
A, B	Probable ribonuclease ZC3H12C	endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity hydrolase activity RNA binding binding nucleic acid binding mRNA binding cation binding transition metal ion binding endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity hydrolase activity RNA binding binding nucleic acid binding mRNA binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	-	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040757	Endoribonuclease Regnase 1/ZC3H12, C-terminal domain	Domain
A, B	IPR000571	Zinc finger, CCCH-type	Domain
A, B	IPR040546	Rege-1, UBA-like domain	Domain
A, B	IPR051101	ZC3H12/N4BP1 Ribonuclease and Regulator	Family
A, B	IPR021869	Ribonuclease Zc3h12a-like, NYN 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.