3P83 | pdb_00003p83

Structure of the PCNA:RNase HII complex from Archaeoglobus fulgidus.

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3p83a1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	automated matches	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
B	d3p83b1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	automated matches	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
C	d3p83c1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	automated matches	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
D	d3p83d1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
D	d3p83d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
E	d3p83e1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
E	d3p83e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)
F	d3p83f_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Archaeoglobus fulgidus ) [TaxId: 2234 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DNA clamp	8040967	3000780	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA clamp	8040969	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8040967	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8040969	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8040969	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8040967	3000780	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8033565	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8033565	3000143	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribonuclease H-like	8033565	3000143	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	PCNA_C	e3p83A2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
A	PCNA_N_1	e3p83A1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N_1	ECOD (1.6)
B	PCNA_C	e3p83B2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
B	PCNA_N_1	e3p83B1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N_1	ECOD (1.6)
C	PCNA_C	e3p83C2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
C	PCNA_N_1	e3p83C1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_N_1	ECOD (1.6)
D	RNase_HII	e3p83D1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_HII	ECOD (1.6)
E	RNase_HII	e3p83E1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_HII	ECOD (1.6)
F	RNase_HII	e3p83F1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_HII	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
B	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
C	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
E	1.10.10.460	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ribonuclease hii. Domain 2	CATH (4.3.0)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
F	1.10.10.460	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Ribonuclease hii. Domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02747	Proliferating cell nuclear antigen, C-terminal domain (PCNA_C)	Proliferating cell nuclear antigen, C-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
A, B, C	PF00705	Proliferating cell nuclear antigen, N-terminal domain (PCNA_N)	Proliferating cell nuclear antigen, N-terminal domain	N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.	Domain
D, E, F	PF01351	Ribonuclease HII (RNase_HII)	Ribonuclease HII	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	DNA polymerase sliding clamp	DNA binding binding nucleic acid binding enzyme regulator activity molecular function activator activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA polymerase processivity factor activity enzyme activator activity catalytic activity, acting on DNA DNA polymerase activity molecular function regulator activity DNA binding binding nucleic acid binding enzyme regulator activity molecular function activator activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA polymerase processivity factor activity enzyme activator activity catalytic activity, acting on DNA DNA polymerase activity molecular function regulator activity catalytic activity	DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process regulation of biological process regulation of cellular process DNA-templated DNA replication primary metabolic process DNA metabolic process leading strand elongation nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process regulation of primary metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process	-
D, E, F	Ribonuclease HII	cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity cation binding manganese ion binding transition metal ion binding ion binding binding metal ion binding small molecule binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity catalytic activity RNA binding nucleic acid binding	DNA replication, removal of RNA primer catabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA replication nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process DNA replication, removal of RNA primer catabolic process RNA metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA replication nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR046938	DNA clamp superfamily	Homologous Superfamily
A, B, C	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
A, B, C	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
A, B, C	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
A, B, C	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
D, E, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
D, E, F	IPR020787	Ribonuclease HII, archaea	Family
D, E, F	IPR004649	Ribonuclease H2, subunit A	Family
D, E, F	IPR024567	Ribonuclease HII/HIII domain	Domain
D, E, F	IPR001352	Ribonuclease HII/HIII	Family
D, E, F	IPR023160	Ribonuclease HII, helix-loop-helix cap domain superfamily	Homologous Superfamily
D, E, F	IPR012337	Ribonuclease H-like 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.