7N9X | pdb_00007n9x

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
I [auth III]	SCOP2B Superfamily	Cyclophilin-like	8043341	3000168	SCOP2B (2022-06-29)
H [auth HHH]	SCOP2B Superfamily	Cyclophilin-like	8043341	3000168	SCOP2B (2022-06-29)
G [auth GGG]	SCOP2B Superfamily	Cyclophilin-like	8043341	3000168	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)
I [auth III]	Pro_isomerase	e7n9xIII1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)
H [auth HHH]	Pro_isomerase	e7n9xHHH1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)
G [auth GGG]	Pro_isomerase	e7n9xGGG1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)
F [auth DDD]	V-set_10	e7n9xDDD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
E [auth EEE]	V-set_8	e7n9xEEE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth FFF]	V-set_8	e7n9xFFF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth AAA]	Gag_p24_C	e7n9xAAA2	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 [auth AAA]	Gag_p24_N	e7n9xAAA1	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 [auth CCC]	Gag_p24_C	e7n9xCCC1	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 [auth CCC]	Gag_p24_N	e7n9xCCC2	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 [auth BBB]	Gag_p24_C	e7n9xBBB2	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 [auth BBB]	Gag_p24_N	e7n9xBBB1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth GGG], H [auth HHH], I [auth III]	PF00160	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase)	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD	The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ...	The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1].	Domain
A [auth BBB], B [auth CCC], C [auth AAA]	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 [auth BBB], B [auth CCC], C [auth AAA]	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
G [auth GGG], H [auth HHH], I [auth III]	Peptidyl-prolyl cis-trans isomerase A	amide binding binding cyclosporin A binding isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity glycosaminoglycan binding organic acid binding ion binding heparan sulfate binding anion binding carboxylic acid binding amide binding binding cyclosporin A binding isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity glycosaminoglycan binding organic acid binding ion binding heparan sulfate binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding sulfur compound binding RNA binding nucleic acid binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding unfolded protein binding virion binding	cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of stress-activated MAPK cascade negative regulation of biological process regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication stress-activated MAPK cascade cellular response to stress cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of stress-activated MAPK cascade negative regulation of biological process regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation regulation of stress-activated protein kinase signaling cascade regulation of MAPK cascade negative regulation of signal transduction regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus negative regulation of stress-activated protein kinase signaling cascade MAPK cascade regulation of cell communication cellular process negative regulation of MAPK cascade regulation of apoptotic process regulation of programmed cell death cell death apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process activation of protein kinase B activity positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of cellular process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process cell chemotaxis chemotaxis neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion negative regulation of phosphate metabolic process negative regulation of protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process negative regulation of phosphorylation multicellular organismal process regulation of body fluid levels wound healing homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion coagulation regulation of biological quality response to wounding platelet activation response to oxidative stress cellular response to oxidative stress cellular response to chemical stress negative regulation of catalytic activity negative regulation of kinase activity negative regulation of molecular function negative regulation of protein kinase activity negative regulation of viral process regulation of viral process regulation of viral life cycle negative regulation of viral life cycle viral process viral life cycle positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription cellular component organization organelle organization lipid droplet organization cellular component organization or biogenesis positive regulation of viral genome replication positive regulation of viral process viral genome replication regulation of viral genome replication peptidyl-amino acid modification peptidyl-proline modification protein peptidyl-prolyl isomerization developmental process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development system development negative regulation of post-translational protein modification regulation of protein K48-linked ubiquitination regulation of protein ubiquitination protein ubiquitination regulation of protein modification by small protein conjugation or removal negative regulation of protein ubiquitination regulation of protein polyubiquitination negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein polyubiquitination negative regulation of protein K48-linked ubiquitination negative regulation of protein polyubiquitination post-translational protein modification protein modification by small protein conjugation protein K48-linked ubiquitination protein modification by small protein conjugation or removal positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of MAPK cascade positive regulation of intracellular signal transduction positive regulation of signaling regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization regulation of secretion by cell secretion by cell positive regulation of secretion intracellular protein localization regulation of transport secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport macromolecule localization positive regulation of protein localization intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of programmed cell death negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process exit from host cell biological process involved in interspecies interaction between organisms viral release from host cell biological process involved in interaction with host biological process involved in symbiotic interaction cell adhesion molecule production endothelial cell activation	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol anchoring junction cell junction focal adhesion cell-substrate junction membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle protein-containing complex vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus
F [auth DDD]	Nanobody	-	-	-
E [auth EEE]	Nanobody	-	-	-
D [auth FFF]	Nanobody	-	-	-
A [auth BBB], B [auth CCC], C [auth AAA]	Capsid protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA 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 host multivesicular body other organism part 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 host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth GGG], H [auth HHH], I [auth III]	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
G [auth GGG], H [auth HHH], I [auth III]	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
G [auth GGG], H [auth HHH], I [auth III]	IPR024936	Cyclophilin-type peptidyl-prolyl cis-trans isomerase	Family
G [auth GGG], H [auth HHH], I [auth III]	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site	Conserved Site
A [auth BBB], B [auth CCC], C [auth AAA]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A [auth BBB], B [auth CCC], C [auth AAA]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A [auth BBB], B [auth CCC], C [auth AAA]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A [auth BBB], B [auth CCC], C [auth AAA]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A [auth BBB], B [auth CCC], C [auth AAA]	IPR001878	Zinc finger, CCHC-type	Domain
A [auth BBB], B [auth CCC], C [auth AAA]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A [auth BBB], B [auth CCC], C [auth AAA]	IPR010999	Retroviral matrix protein	Homologous Superfamily
A [auth BBB], B [auth CCC], C [auth AAA]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A [auth BBB], B [auth CCC], C [auth AAA]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth GGG], H [auth HHH], I [auth III]	Pharos: P62937	squamous cell carcinoma non-small cell lung carcinoma Neoplasm Metastasis rheumatoid arthritis breast cancer gastric neoplasm mucocutaneous lymph node syndrome ovarian cancer peripheral nervous system disease schizophrenia dry eye syndrome hereditary diffuse gastric adenocarcinoma myopathy oral cavity neoplasm pancreatic intraductal papillary-mucinous carcinoma squamous cell carcinoma non-small cell lung carcinoma Neoplasm Metastasis rheumatoid arthritis breast cancer gastric neoplasm mucocutaneous lymph node syndrome ovarian cancer peripheral nervous system disease schizophrenia dry eye syndrome hereditary diffuse gastric adenocarcinoma myopathy oral cavity neoplasm pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy gastric cancer juvenile dermatomyositis osteosarcoma 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.