6T8H | pdb_00006t8h

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
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)
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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase 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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity 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 cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation 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 cellular process macromolecule metabolic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex
G [auth T]	DNA template	-	-	-
F [auth P]	DNA primer	-	-	-
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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase 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 nucleic acid binding DNA exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity 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 cellular process macromolecule metabolic process intein-mediated protein splicing gene expression 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 cellular process macromolecule metabolic process intein-mediated protein splicing gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process protein splicing DNA-templated DNA replication DNA replication	-
A [auth E], D [auth C], E [auth D]	DNA polymerase sliding clamp	DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein binding	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR054750	DNA polymerase II small subunit, N-terminal domain	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]	IPR004843	Calcineurin-like, phosphoesterase domain	Domain
B [auth A]	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
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]	IPR006141	Intein N-terminal splicing region	PTM
C [auth B]	IPR056171	DNA polymerase II large subunit DP2, central domain	Domain
C [auth B]	IPR056172	DNA polymerase II large subunit DP2, catalytic domain	Domain
C [auth B]	IPR003587	Hint domain N-terminal	Domain
C [auth B]	IPR004475	DNA polymerase II large subunit DP2	Family
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

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.