6T8H

Cryo-EM structure of the DNA-bound PolD-PCNA processive complex from P. abyssi

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 [auth A]	SCOP2B Superfamily	Metallo-dependent phosphatases	8053389	3001067	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8053391	3000135	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8055689	3001330	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 [auth E]	PCNA_C	e6t8hE1	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 [auth E]	PCNA_N_1	e6t8hE2	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 [auth C]	PCNA_C	e6t8hC1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
D [auth C]	PCNA_N_1	e6t8hC2	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)
E [auth D]	PCNA_C	e6t8hD1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: PCNA_C	ECOD (1.6)
E [auth D]	PCNA_N_1	e6t8hD2	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 [auth A]	tRNA_anti-codon	e6t8hA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: tRNA_anti-codon	ECOD (1.6)
B [auth A]	DNA_pol_E_B	e6t8hA2	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: DNA_pol_E_B	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth E]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (utative)
D [auth C]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (utative)
E [auth D]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], D [auth C], E [auth D]	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 [auth E], D [auth C], E [auth D]	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
B [auth A]	PF00149	Calcineurin-like phosphoesterase (Metallophos)	Calcineurin-like phosphoesterase	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or ...	This family includes a diverse range of phosphoesterases [1], including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD Swiss:P13457 or yeast MRE11 Swiss:P32829. The most conserved regions in this superfamily centre around the metal chelating residues.	Domain
C [auth B]	PF03833	DNA polymerase II large subunit DP2 (PolC_DP2)	DNA polymerase II large subunit DP2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], D [auth C], E [auth D]	DNA polymerase sliding clamp	DNA binding binding organic cyclic compound binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity	nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of biological 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 nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process regulation of biological 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	-
B [auth A]	DNA polymerase II small subunit	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic 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 catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process DNA-templated DNA replication DNA replication	-
C [auth B]	DP2 subunit of D-family DNA-polymerase	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity	catabolic 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 catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process intein-mediated protein splicing cellular biosynthetic process cellular metabolic process catabolic 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 catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process intein-mediated protein splicing cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing cellular process protein metabolic process protein splicing DNA-templated DNA replication DNA replication	-
F [auth P]	DNA primer	-	-	-
G [auth T]	DNA template	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], D [auth C], E [auth D]	IPR046938	DNA clamp superfamily	Homologous Superfamily
A [auth E], D [auth C], E [auth D]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
A [auth E], D [auth C], E [auth D]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
A [auth E], D [auth C], E [auth D]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
A [auth E], D [auth C], E [auth D]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
B [auth A]	IPR004843	Calcineurin-like phosphoesterase domain, ApaH type	Domain
B [auth A]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B [auth A]	IPR011149	DNA polymerase II small subunit, archaeal	Family
B [auth A]	IPR024826	DNA polymerase delta/II small subunit family	Family
B [auth A]	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
C [auth B]	IPR006141	Intein N-terminal splicing region	PTM
C [auth B]	IPR016033	DNA polymerase II large subunit DP2, N-terminal	Domain
C [auth B]	IPR036844	Hint domain superfamily	Homologous Superfamily
C [auth B]	IPR030934	Intein C-terminal splicing region	Conserved Site
C [auth B]	IPR003587	Hint domain N-terminal	Domain
C [auth B]	IPR004475	DNA polymerase II large subunit DP2	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.