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	RNase_Zc3h12a	e7ndjB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: RNase_Zc3h12a	ECOD (1.6)
B	zf-CCCH_2_2	e7ndjB2	A: few secondary structure elements	X: CCCH zinc finger	H: CCCH zinc finger (From Topology)	T: CCCH zinc finger	F: zf-CCCH_2_2	ECOD (1.6)
A	RNase_Zc3h12a	e7ndjA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: RNase_Zc3h12a	ECOD (1.6)

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 a nucleic acid catalytic activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	-	-

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.