5DMR

Crystal Structure of C-terminal domain of mouse eRF1 in complex with RNase H domain of RT of Moloney Murine Leukemia Virus

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)
A	d5dmra_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	MoMLV (Moloney murine leukemia virus isolate Shinnick ) [TaxId: 928306 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ribonuclease H-like	8075089	4000541	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8075090	3000143	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)
A	PF00075	e5dmrA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00075	ECOD (1.6)
B	PF03465	e5dmrB1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: PF03465	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00075	RNase H (RNase_H)	RNase H	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.	Domain
B	PF03465	eRF1 domain 3 (eRF1_3)	eRF1 domain 3	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The o ...	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Reverse transcriptase/ribonuclease H p80	endonuclease activity retroviral integrase activity integrase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity retroviral 3' processing activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity RNA binding binding endonuclease activity retroviral integrase activity integrase activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity retroviral 3' processing activity DNA endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity RNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity RNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters RNA-directed DNA polymerase activity structural constituent of virion structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process catabolic process primary metabolic process DNA metabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process organic substance catabolic process virion assembly viral process viral life cycle establishment of integrated proviral latency viral latency establishment of viral latency viral genome integration into host DNA DNA recombination symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular membrane-bounded organelle host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell late endosome host cell endosome membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular membrane-bounded organelle host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell late endosome host cell endosome host intracellular region host cell late endosome membrane host cell endosome membrane protein-containing complex protein-DNA complex viral nucleocapsid viral capsid virion component
B	Eukaryotic peptide chain release factor subunit 1	translation release factor activity, codon specific translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding aminoacyl-tRNA hydrolase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity translation release factor activity, codon specific translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding aminoacyl-tRNA hydrolase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity RNA binding sequence-specific mRNA binding mRNA binding	cytoplasmic translational termination cellular biosynthetic process organonitrogen compound biosynthetic process protein-containing complex disassembly cellular component organization organic substance metabolic process organic substance biosynthetic process translational termination cellular component organization or biogenesis protein metabolic process cellular component disassembly organonitrogen compound metabolic process protein-containing complex organization cellular metabolic process cytoplasmic translational termination cellular biosynthetic process organonitrogen compound biosynthetic process protein-containing complex disassembly cellular component organization organic substance metabolic process organic substance biosynthetic process translational termination cellular component organization or biogenesis protein metabolic process cellular component disassembly organonitrogen compound metabolic process protein-containing complex organization cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cytoplasmic translation cellular process metabolic process macromolecule metabolic process regulation of cellular process regulation of cellular component organization regulation of protein-containing complex disassembly regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of translational termination biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process organic substance catabolic process	intracellular organelle intracellular anatomical structure cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytoplasm cellular anatomical entity cytosol non-membrane-bounded organelle protein-containing complex translation release factor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR040643	Murine leukemia virus integrase, C-terminal	Domain
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A	IPR001878	Zinc finger, CCHC-type	Domain
A	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A	IPR010999	Retroviral matrix protein	Homologous Superfamily
A	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A	IPR002079	Gag polyprotein, inner coat protein p12	Domain
A	IPR001969	Aspartic peptidase, active site	Active Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR018061	Retropepsins	Domain
A	IPR002156	Ribonuclease H domain	Domain
A	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A	IPR000840	Gamma-retroviral matrix protein	Domain
A	IPR001584	Integrase, catalytic core	Domain
A	IPR041577	Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR000477	Reverse transcriptase domain	Domain
A	IPR036946	Gamma-retroviral matrix domain superfamily	Homologous Superfamily
A	IPR039464	Gag-Pol polyprotein, Zinc-finger like domain	Domain
A	IPR003036	Core shell protein Gag P30	Domain
B	IPR004403	Peptide chain release factor eRF1/aRF1	Family
B	IPR005141	eRF1 domain 2	Domain
B	IPR005140	eRF1 domain 1/Pelota-like	Domain
B	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
B	IPR024049	eRF1, domain 1	Homologous Superfamily
B	IPR005142	eRF1 domain 3	Domain
B	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily