7N9V | pdb_00007n9v

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth K]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
E [auth I]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
A [auth C]	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)
K [auth H]	V-set_8	e7n9vH1	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)
L	V-set_8	e7n9vL1	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)
J [auth F]	V-set_8	e7n9vF1	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)
I [auth E]	V-set_8	e7n9vE1	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)
H [auth B]	V-set_8	e7n9vB1	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)
G [auth J]	V-set_8	e7n9vJ1	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)
F [auth K]	Gag_p24_C	e7n9vK1	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 [auth K]	Gag_p24_N	e7n9vK2	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 [auth I]	Gag_p24_C	e7n9vI1	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 [auth I]	Gag_p24_N	e7n9vI2	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 [auth G]	Gag_p24_C	e7n9vG2	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 [auth G]	Gag_p24_N	e7n9vG1	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 [auth D]	Gag_p24_C	e7n9vD1	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 D]	Gag_p24_N	e7n9vD2	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 A]	Gag_p24_C	e7n9vA1	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 A]	Gag_p24_N	e7n9vA2	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 C]	Gag_p24_C	e7n9vC1	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 C]	Gag_p24_N	e7n9vC2	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)
K [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
J [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
I [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
H [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
G [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F [auth K]	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (utative)
F [auth K]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)
E [auth I]	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (utative)
E [auth I]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)
D [auth G]	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (utative)
D [auth G]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)
C [auth D]	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (utative)
C [auth D]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)
B [auth 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)
B [auth A]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)
A [auth C]	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 [auth C]	1.10.1200.30	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth J], H [auth B], I [auth E], J [auth F], K [auth H], G [auth J], H [auth B], I [auth E], J [auth F], K [auth H], L	Heavy Chain	IGHV1	-	capsid protein	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	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 C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	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 J], H [auth B], I [auth E], J [auth F], K [auth H], G [auth J], H [auth B], I [auth E], J [auth F], K [auth H], L	Nanobody-GYAR	-	-	-
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	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 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
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR001878	Zinc finger, CCHC-type	Domain
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR010999	Retroviral matrix protein	Homologous Superfamily
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	IPR014817	Gag protein p6	Domain
A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], A [auth C], B [auth A], C [auth D], D [auth G], E [auth I], F [auth K]	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.