3P56 | pdb_00003p56

The structure of the human RNase H2 complex defines key interaction interfaces relevant to enzyme function and human disease

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Rap30/74 heterodimerisation domain-like	8086854	3000142	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rap30/74 heterodimerisation domain-like	8086854	3000142	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8098224	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8098224	3000143	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)
F	RNase_H2_suC	e3p56F1	A: a/b three-layered sandwiches	X: Suppressor of Fused, C-terminal domain	H: HTH	T: winged helix domain	F: RNase_H2_suC	ECOD (v294.1)
C	RNase_H2_suC	e3p56C1	A: a/b three-layered sandwiches	X: Uncharacterized protein CV_1783	H: triple barrel	T: RNase H2 subunits B and C	F: RNase_H2_suC	ECOD (v294.1)
E		e3p56E3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F:	ECOD (v294.1)
E	Acetyltransf_1	e3p56E2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acetyltransf_1	ECOD (v294.1)
B	RNase_H2-Ydr279	e3p56B2	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: RNA-binding domain, RBD	T: RNA-binding domain, RBD	F: RNase_H2-Ydr279	ECOD (v294.1)
B	RNase_H2_suC	e3p56B1	A: a/b three-layered sandwiches	X: Uncharacterized protein CV_1783	H: triple barrel	T: RNase H2 subunits B and C	F: RNase_H2_suC	ECOD (v294.1)
D	FAD_binding_4	e3p56D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)
A	FAD_binding_4	e3p56A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: FAD_binding_4	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF08615	Ribonuclease H2 non-catalytic subunit (Ylr154p-like) (RNase_H2_suC)	Ribonuclease H2 non-catalytic subunit (Ylr154p-like)	-	Family
B, E	PF09468	Ydr279p protein family (RNase H2 complex component) wHTH domain (RNase_H2-Ydr279)	Ydr279p protein family (RNase H2 complex component) wHTH domain	RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the ...	RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p [1]. It is not known whether non yeast proteins in this family fulfil the same function.	Domain
B, E	PF17745	Ydr279p protein triple barrel domain (Ydr279_N)	Ydr279p protein triple barrel domain	RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the ...	RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organisms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologues of Ydr279p [1]. It is not known whether non yeast proteins in this family fulfil the same function. This domain corresponds to the N-terminal triple barrel domain.	Domain
A, D	PF01351	Ribonuclease HII (RNase_HII)	Ribonuclease HII		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Ribonuclease H2 subunit C	-	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 cellular response to stimulus mismatch repair 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 cellular response to stimulus mismatch repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair	protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B, E	Ribonuclease H2 subunit B	-	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 biosynthetic process gene expression 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 biosynthetic process gene expression macromolecule biosynthetic process fibroblast proliferation cell population proliferation cellular response to stimulus mismatch repair response to stimulus DNA metabolic process cellular response to stress DNA damage response response to stress DNA repair cell cycle G2/M phase transition regulation of biological process regulation of cell cycle phase transition regulation of cellular process regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process G2/M transition of mitotic cell cycle biological regulation regulation of cell cycle G2/M phase transition cell cycle phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle cell cycle process mitotic cell cycle phase transition ribose phosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative metabolic process nucleotide metabolic process ribonucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process positive regulation of cell population proliferation positive regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation positive regulation of cellular process regulation of biosynthetic process negative regulation of metabolic process negative regulation of biological process regulation of macromolecule metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of macromolecule metabolic process DNA damage checkpoint signaling signaling regulation of cellular response to stress negative regulation of cell cycle regulation of signal transduction intracellular signal transduction cell communication regulation of cell cycle checkpoint regulation of intracellular signal transduction regulation of response to stress negative regulation of cell cycle phase transition signal transduction regulation of signaling DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of response to stimulus signal transduction in response to DNA damage regulation of cell communication regulation of DNA damage checkpoint developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
A, D	Ribonuclease H2 subunit A	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 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 binding nucleic acid binding cation binding ion binding metal ion binding small molecule 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 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 DNA metabolic process DNA replication, removal of RNA primer cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle protein-containing complex catalytic complex intracellular protein-containing complex ribonuclease H2 complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR052863	Ribonuclease H2 subunit C	Family
C, F	IPR013924	Ribonuclease H2, subunit C	Family
B, E	IPR040456	Ribonuclease H2 subunit B	Family
B, E	IPR041195	Rnh202, triple barrel domain	Domain
B, E	IPR019024	Ribonuclease H2 subunit B, wHTH domain	Domain
A, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D	IPR004649	Ribonuclease H2, subunit A	Family
A, D	IPR024567	Ribonuclease HII/HIII domain	Domain
A, D	IPR001352	Ribonuclease HII/HIII	Family
A, D	IPR023160	Ribonuclease HII, helix-loop-helix cap domain superfamily	Homologous Superfamily
A, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: Q8TDP1	Aicardi-Goutieres syndrome Aicardi-Goutieres syndrome 3 acne allergic rhinitis chronic kidney disease heart disease metabolic syndrome X psoriasis systemic lupus erythematosus atopic eczema Dermatomyositis, Childhood Type intellectual disability oligodendroglioma skin basal cell carcinoma tuberculosis Aicardi-Goutieres syndrome Aicardi-Goutieres syndrome 3 acne allergic rhinitis chronic kidney disease heart disease metabolic syndrome X psoriasis systemic lupus erythematosus atopic eczema Dermatomyositis, Childhood Type intellectual disability oligodendroglioma skin basal cell carcinoma tuberculosis breast carcinoma leukodystrophy osteosarcoma subependymal giant cell astrocytoma
B, E	Pharos: Q5TBB1	Aicardi-Goutieres syndrome Aicardi-Goutieres syndrome 2 astrocytic tumor Epileptic encephalopathy malignant mesothelioma pseudo-TORCH syndrome Aicardi-Goutieres syndrome 1 benign prostatic hyperplasia intellectual disability medulloblastoma tuberculosis leukodystrophy osteosarcoma
A, D	Pharos: O75792	Aicardi-Goutieres syndrome Aicardi-Goutieres syndrome 4 medulloblastoma ovarian cancer acute myeloid leukemia Dermatomyositis, Childhood Type glioblastoma invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma non-small cell lung carcinoma primitive neuroectodermal tumor adrenal cortex carcinoma atypical teratoid rhabdoid tumor endometriosis Aicardi-Goutieres syndrome Aicardi-Goutieres syndrome 4 medulloblastoma ovarian cancer acute myeloid leukemia Dermatomyositis, Childhood Type glioblastoma invasive ductal breast carcinoma lung adenocarcinoma malignant ependymoma non-small cell lung carcinoma primitive neuroectodermal tumor adrenal cortex carcinoma atypical teratoid rhabdoid tumor endometriosis hydrocephalus large cell medulloblastoma lung cancer malignant glioma osteosarcoma psoriasis breast cancer intellectual disability leukodystrophy malignant colon neoplasm

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.