6AYA | pdb_00006aya

Structure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	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)
A	Gag_p24_C	e6ayaA2	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	e6ayaA1	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 (utative)
A	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	HIV-1 capsid protein	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation virion assembly viral budding viral budding via host ESCRT complex viral life cycle	host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region membrane virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region membrane virion component virion membrane host cell nucleus host cell plasma membrane host cell membrane viral nucleocapsid viral capsid
B	Nuclear pore complex protein Nup153	molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity nuclear localization sequence binding signal sequence binding binding peptide binding DNA binding nucleic acid binding protein-membrane adaptor activity cation binding ion binding metal ion binding small molecule binding molecular condensate scaffold activity protein-macromolecule adaptor activity molecular adaptor activity nuclear localization sequence binding signal sequence binding binding peptide binding DNA binding nucleic acid binding protein-membrane adaptor activity cation binding ion binding metal ion binding small molecule binding structural molecule activity structural constituent of nuclear pore identical protein binding protein binding	RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport 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 cellular component organization metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process cellular component organization or biogenesis supramolecular fiber organization amyloid fibril formation cellular localization nucleocytoplasmic transport nuclear transport establishment of localization in cell intracellular transport protein localization establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization protein localization to organelle protein import into nucleus intracellular protein transport RNA export from nucleus nuclear export regulation of localization negative regulation of RNA export from nucleus negative regulation of nucleocytoplasmic transport regulation of cellular process negative regulation of biological process negative regulation of transport negative regulation of cellular process regulation of intracellular transport negative regulation of intracellular transport regulation of biological process regulation of transport negative regulation of nucleobase-containing compound transport regulation of nucleobase-containing compound transport regulation of RNA export from nucleus biological regulation regulation of nucleocytoplasmic transport regulation of cellular localization viral penetration into host nucleus intracellular transport of virus transport of virus nuclear pore organization protein-containing complex organization pore complex assembly cellular component biogenesis nuclear pore complex assembly nucleus organization organelle organization cellular component assembly protein-containing complex assembly	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane organelle envelope nuclear envelope endomembrane system nuclear membrane organelle membrane cytoplasm cytosol nuclear periphery protein-containing complex nuclear protein-containing complex nuclear pore nucleoplasm nuclear pore nuclear basket host cellular component host cell inclusion body nuclear inclusion body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A	IPR001878	Zinc finger, CCHC-type	Domain
A	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A	IPR010999	Retroviral matrix protein	Homologous Superfamily
A	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A	IPR014817	Gag protein p6	Domain
A	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
B	IPR013913	Nucleoporin Nup153, N-terminal	Domain
B	IPR026054	Nuclear pore complex protein	Family
B	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
B	IPR018892	Retro-transposon transporting motif	Conserved Site
B	IPR001876	Zinc finger, RanBP2-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P49790	amyotrophic lateral sclerosis lymphoplasmacytic lymphoma ovarian cancer dermatomyositis medulloblastoma plasma cell myeloma interstitial lung disease osteosarcoma psoriasis

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.