3FDS | pdb_00003fds

Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

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)
C [auth D]	d3fdsd1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	automated matches	automated matches	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
A	d3fdsa2	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	DinB homolog (DBH)	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)
A	d3fdsa1	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DinB homolog (DBH)	(Saccharolobus solfataricus ) [TaxId: 2287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ta1206-like	8055757	3001431	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	3000579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	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)
C [auth D]	IL7	e3fdsD1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
B [auth C]	IL7	e3fdsC1	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
A	IL7	e3fdsA2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (develop294)
A	SidM_Rab1-act	e3fdsA5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: SidM_Rab1-act	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
B [auth C]	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
A	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [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 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
A	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
A	PF11799	impB/mucB/samB family C-terminal domain (IMS_C)	impB/mucB/samB family C-terminal domain	These proteins are involved in UV protection (Swiss).	Domain
A	PF11798	IMS family HHH motif (IMS_HHH)	IMS family HHH motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	DNA polymerase sliding clamp C	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	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	-
B [auth C]	DNA polymerase sliding clamp B	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	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	-
A	DNA polymerase IV	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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding damaged DNA binding nucleic acid binding	translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress DNA damage response response to stress metabolic process cellular process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA repair DNA-templated DNA replication	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR046938	DNA clamp superfamily	Homologous Superfamily
C [auth D]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
C [auth D]	IPR022649	Proliferating cell nuclear antigen, PCNA, C-terminal	Domain
C [auth D]	IPR022659	Proliferating cell nuclear antigen, PCNA, conserved site	Conserved Site
C [auth D]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
B [auth C]	IPR046938	DNA clamp superfamily	Homologous Superfamily
B [auth C]	IPR000730	Proliferating cell nuclear antigen, PCNA	Family
B [auth C]	IPR022648	Proliferating cell nuclear antigen, PCNA, N-terminal	Domain
A	IPR001126	UmuC domain	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR050116	DNA polymerase type-Y	Family
A	IPR022880	DNA polymerase IV	Family
A	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
A	IPR024728	DNA polymerase type-Y, HhH motif	Conserved Site

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.