4B4N | pdb_00004b4n

CPSF6 defines a conserved capsid interface that modulates HIV-1 replication

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	d4b4na_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	automated matches	(Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8101363	3000745	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)
A	Gag_p24_N	e4b4nA1	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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 6	RNA binding binding nucleic acid binding mRNA binding ribonucleoprotein complex binding protein-containing complex binding ribosomal large subunit binding ribosome binding exon-exon junction complex binding	protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization regulation of localization cellular localization nitrogen compound transport protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular process cellular component organization or biogenesis protein heterooligomerization regulation of localization cellular localization nitrogen compound transport regulation of cellular process nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of biological process positive regulation of nucleobase-containing compound transport localization positive regulation of RNA export from nucleus establishment of localization in cell positive regulation of intracellular transport RNA localization nuclear export nucleobase-containing compound transport positive regulation of cellular process regulation of intracellular transport regulation of biological process RNA transport regulation of transport regulation of nucleobase-containing compound transport regulation of RNA export from nucleus nucleic acid transport biological regulation intracellular transport regulation of nucleocytoplasmic transport establishment of localization RNA export from nucleus establishment of RNA localization positive regulation of transport regulation of cellular localization macromolecule localization mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process mRNA alternative polyadenylation RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process RNA processing macromolecule metabolic process co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle membrane-enclosed lumen perichromatin fibrils nuclear chromosome intracellular membraneless organelle membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle membrane-enclosed lumen perichromatin fibrils nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen membrane nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule paraspeckles cytoplasm interchromatin granule ribonucleoprotein complex mRNA cleavage and polyadenylation specificity factor complex
A	GAG PROTEIN	RNA binding binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell plasma membrane host cell membrane viral nucleocapsid viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell plasma membrane host cell membrane viral nucleocapsid viral capsid virion component host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR057951	CPSF6/7, RSLD domain, N-terminal region	Domain
B	IPR000504	RNA recognition motif domain	Domain
B	IPR034772	CPSF6/7	Family
B	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
B	IPR034769	Cleavage and polyadenylation specificity factor subunit 6, RNA recognition motif	Domain
A	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q16630	astrocytic tumor diabetes mellitus lung cancer myopathy pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma attention deficit hyperactivity disorder, inattentive type glioblastoma malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor IgA glomerulonephritis medulloblastoma astrocytic tumor diabetes mellitus lung cancer myopathy pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma attention deficit hyperactivity disorder, inattentive type glioblastoma malignant mesothelioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor IgA glomerulonephritis medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.