3PRP | pdb_00003prp

Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin

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)
D	d3prpd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3prpb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	Ubiquitin	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)
D	SCOP2 Family	Ubiquitin-related	8100609	4000962	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Ubiquitin-like	8100610	3000157	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8104287	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8104287	3000157	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)
D	ubiquitin_1	e3prpD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
B	ubiquitin_1	e3prpB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: ubiquitin_1	ECOD (1.6)
C	OTU	e3prpC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: OTU	ECOD (1.6)
A	OTU	e3prpA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: OTU	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.90.70.80	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)
A	3.90.70.80	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain
A, C	PF02338	OTU-like cysteine protease (OTU)	OTU-like cysteine protease	This domain is found in a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly ...	This domain is found in a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases. This domain, despite containing a complete catalytic triad, do not react with Ub propargylamide and has no deubiquitinase activity [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Polyubiquitin-B (Fragment)	-	-	membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane membrane-bounded organelle intracellular anatomical structure mitochondrial membrane mitochondrion membrane organelle outer membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle organelle mitochondrial envelope mitochondrial outer membrane outer membrane cytoplasm organelle membrane nucleus
A, C	RNA-directed RNA polymerase L	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA-directed RNA polymerase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding ion binding metal ion binding	cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral gene expression viral process viral transcription RNA-templated viral transcription symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation symbiont-mediated perturbation of host immune response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host innate immune response protein deubiquitination protein modification by small protein removal macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation or removal symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity symbiont-mediated suppression of host pathogen-associated molecular pattern receptor signaling pathway symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of cytoplasmic pattern recognition receptor signaling pathway RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process viral life cycle negative stranded viral RNA replication viral genome replication viral RNA genome replication symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway regulation of biological process cellular response to topologically incorrect protein regulation of cellular process signaling biological regulation endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication response to topologically incorrect protein signal transduction	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR019956	Ubiquitin domain	Domain
B, D	IPR019954	Ubiquitin conserved site	Conserved Site
B, D	IPR050158	Ubiquitin and ubiquitin-like	Family
B, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B, D	IPR000626	Ubiquitin-like domain	Domain
A, C	IPR015843	RNA-directed RNA polymerase, nairovirus	Family
A, C	IPR007099	RNA-directed RNA polymerase, negative-strand RNA virus	Domain
A, C	IPR029124	RNA-directed RNA polymerase L, N-terminal	Domain
A, C	IPR007322	RNA-dependent RNA polymerase, bunyaviral	Domain
A, C	IPR003323	OTU domain	Domain
A, C	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, C	IPR049605	RNA-directed RNA polymerase L, OTU 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.