3BSU | pdb_00003bsu

Hybrid-binding domain of human RNase H1 in complex with 12-mer RNA/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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
J [auth H]	d3bsuh1	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	L9 N-domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J [auth H]	d3bsuh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I [auth G]	d3bsug_	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	L9 N-domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d3bsuf1	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	L9 N-domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth F]	d3bsuf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth C]	d3bsuc_	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	L9 N-domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth B]	d3bsub1	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	L9 N-domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth B]	d3bsub2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth A]	d3bsua1	Alpha and beta proteins (a+b)	MbtH/L9 domain-like	L9 N-domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth A]	d3bsua2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J [auth H]	SCOP2B Superfamily	L9 N-domain-like	8084343	3000338	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	L9 N-domain-like	8084343	3000338	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	L9 N-domain-like	8084343	3000338	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	L9 N-domain-like	8084343	3000338	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	L9 N-domain-like	8084343	3000338	SCOP2B (2022-06-29)
E [auth A]	SCOP2 Family	N-terminal domain of RNase HI	8084342	4001760	SCOP2 (2022-06-29)
E [auth A]	SCOP2 Superfamily	L9 N-domain-like	8084343	3000338	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J [auth H]	Cauli_VI	e3bsuH1	A: a+b two layers	X: L9 N-domain-like	H: L9 N-domain-like (From Topology)	T: L9 N-domain-like	F: Cauli_VI	ECOD (1.6)
I [auth G]	Cauli_VI	e3bsuG1	A: a+b two layers	X: L9 N-domain-like	H: L9 N-domain-like (From Topology)	T: L9 N-domain-like	F: Cauli_VI	ECOD (1.6)
H [auth F]	Cauli_VI	e3bsuF1	A: a+b two layers	X: L9 N-domain-like	H: L9 N-domain-like (From Topology)	T: L9 N-domain-like	F: Cauli_VI	ECOD (1.6)
G [auth C]	Cauli_VI	e3bsuC1	A: a+b two layers	X: L9 N-domain-like	H: L9 N-domain-like (From Topology)	T: L9 N-domain-like	F: Cauli_VI	ECOD (1.6)
F [auth B]	Cauli_VI	e3bsuB1	A: a+b two layers	X: L9 N-domain-like	H: L9 N-domain-like (From Topology)	T: L9 N-domain-like	F: Cauli_VI	ECOD (1.6)
E [auth A]	Cauli_VI	e3bsuA1	A: a+b two layers	X: L9 N-domain-like	H: L9 N-domain-like (From Topology)	T: L9 N-domain-like	F: Cauli_VI	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth H]	3.40.970.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease HI	Chain A	CATH (4.3.0)
I [auth G]	3.40.970.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease HI	Chain A	CATH (4.3.0)
H [auth F]	3.40.970.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease HI	Chain A	CATH (4.3.0)
G [auth C]	3.40.970.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease HI	Chain A	CATH (4.3.0)
F [auth B]	3.40.970.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease HI	Chain A	CATH (4.3.0)
E [auth A]	3.40.970.10	Alpha Beta	3-Layer(aba) Sandwich	Ribonuclease HI	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	PF01693	Ribonuclease H1 N-terminal domain (Cauli_VI)	Ribonuclease H1 N-terminal domain	This domain is found at the N-terminal of ribonuclease H1 from human, its fungal orthologues and in various caulimovirus viroplasmin proteins. This domain consists of three-stranded antiparallel beta-sheet and two short alpha-helices that pack onto o ...	This domain is found at the N-terminal of ribonuclease H1 from human, its fungal orthologues and in various caulimovirus viroplasmin proteins. This domain consists of three-stranded antiparallel beta-sheet and two short alpha-helices that pack onto opposite faces of the beta-sheet [3] and is structurally similar to ribosomal protein L9 which binds to 23 S ribosomal RNA. RNase H1 belong to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms [2]. Inclusions are the site of viral assembly, DNA synthesis and accumulation [2]. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	Ribonuclease H1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nucleic acid binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity hydrolase activity hydrolase activity, acting on ester bonds RNA endonuclease activity RNA binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process DNA replication, removal of RNA primer DNA metabolic process catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process DNA replication, removal of RNA primer DNA metabolic process DNA replication	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
B [auth E], D [auth J]	DNA (5'-D(DGPDAPDAPDTPDCPDAPDGPDGP(5IU)PDGPDTPDC)-3')	-	-	-
A [auth D], C [auth I]	RNA (5'-R(GPAPCPAPCPCPUPGPAPUPUPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR037056	Ribonuclease H1, N-terminal domain superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR002156	Ribonuclease H domain	Domain
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR050092	Ribonuclease H	Family
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR011320	Ribonuclease H1, N-terminal	Domain
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR009027	Large ribosomal subunit protein bL9/RNase H1, N-terminal	Homologous Superfamily
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR017067	Ribonuclease H1, eukaryote	Family
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], E [auth A], F [auth B], G [auth C], H [auth F], I [auth G], J [auth H]	Pharos: O60930	progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 2 progressive external ophthalmoplegia adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy muscle tissue disease osteosarcoma lung cancer muscular disease ovarian cancer psoriasis Mitochondrial Diseases myopathy

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.