4PH0 | pdb_00004ph0

capsid protein from bovine 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)
F	d4ph0f2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
F	d4ph0f1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
E	d4ph0e2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
E	d4ph0e1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
D	d4ph0d2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
D	d4ph0d1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
C	d4ph0c2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
C	d4ph0c1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
B	d4ph0b2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
B	d4ph0b1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
A	d4ph0a2	All alpha proteins	Acyl carrier protein-like	Retrovirus capsid dimerization domain-like	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)
A	d4ph0a1	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	automated matches	BLV (Bovine leukemia virus ) [TaxId: 11901 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077072	3001819	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	Gag_p24_C	e4ph0F1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
F	Gag_p24_N	e4ph0F2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
E	Gag_p24_C	e4ph0E1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
E	Gag_p24_N	e4ph0E2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
D	Gag_p24_C	e4ph0D1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
D	Gag_p24_N	e4ph0D2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
C	Gag_p24_C	e4ph0C2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
C	Gag_p24_N	e4ph0C1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
B	Gag_p24_C	e4ph0B2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
B	Gag_p24_N	e4ph0B1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
A	Gag_p24_C	e4ph0A1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
A	Gag_p24_N	e4ph0A2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
F	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
E	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
E	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
D	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
D	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
C	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
C	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
B	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
B	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
A	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
A	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00607	gag protein p24 N-terminal domain (Gag_p24)	gag protein p24 N-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain
A, B, C, D, E A, B, C, D, E, F	PF19317	Gag protein p24 C-terminal domain (Gag_p24_C)	Gag protein p24 C-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	BLV capsid	DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity catalytic activity, acting on DNA DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding RNA stem-loop binding structural constituent of virion structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA virion assembly viral budding viral budding via host ESCRT complex nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA integration proteolysis protein metabolic process	viral nucleocapsid viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003139	Delta-retroviral matrix protein	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR018061	Retropepsins	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

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.