2R8J | pdb_00002r8j

Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin containing DNA

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)
E [auth A]	d2r8ja1	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E [auth A]	d2r8ja2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DNA polymerase eta	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E [auth A]	d2r8ja3	Artifacts	Tags	Tags	Tags	N-terminal Tags	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth B]	d2r8jb1	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	automated matches	automated matches	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth B]	d2r8jb2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DNA polymerase eta	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035582	3000579	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035585	3001272	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Ta1206-like	8055756	3001431	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035585	3001272	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035585	3001272	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Ta1206-like	8055756	3001431	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035585	3001272	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035582	3000579	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)
E [auth A]	IMS_HHH_1	e2r8jA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.1)
E [auth A]	OKR_DC_1_C	e2r8jA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
E [auth A]	RNase_P_Rpp14	e2r8jA3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
E [auth A]	Pkinase	e2r8jA4	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Pkinase	ECOD (v294.1)
F [auth B]	IMS_HHH_1	e2r8jB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.1)
F [auth B]	OKR_DC_1_C	e2r8jB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
F [auth B]	RNase_P_Rpp14	e2r8jB3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
F [auth B]	Pkinase	e2r8jB4	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Pkinase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
E [auth A]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
E [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
E [auth A]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
F [auth B]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
F [auth B]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
F [auth B]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F [auth B]	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
E [auth A], F [auth B]	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
E [auth A], F [auth B]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B]	DNA polymerase eta	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 transition metal ion binding zinc ion binding ion binding binding metal ion 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 transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding DNA binding damaged DNA binding nucleic acid binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA biosynthetic process DNA repair error-free translesion synthesis cellular component organization organelle organization mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion cellular component organization or biogenesis cell cycle cell cycle process chromosome segregation response to radiation response to abiotic stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membraneless organelle replication fork intracellular membraneless organelle chromosome site of double-strand break site of DNA damage membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membraneless organelle replication fork intracellular membraneless organelle chromosome site of double-strand break site of DNA damage nucleus
B [auth U], D [auth T]	DNA (5'-D(PDGPDGPDCPDTPDCPDAPDTPDCPDCPDAP*DC)-3')	-	-	-
A [auth Q], C [auth P]	DNA (5'-D(DGPDTPDGPDGPDAPDTPDGPDAP*DG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR041298	DNA polymerase eta, ubiquitin-binding zinc finger	Domain
E [auth A], F [auth B]	IPR001126	UmuC domain	Domain
E [auth A], F [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
E [auth A], F [auth B]	IPR052230	DNA polymerase eta	Family
E [auth A], F [auth B]	IPR017961	DNA polymerase, Y-family, little finger 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.