4LAJ | pdb_00004laj

Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic miniprotein, M48U1, and llama single-domain, broadly neutralizing, co-receptor binding site antibody, JM4

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L [auth I]	Asp	e4lajI1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: Asp	ECOD (v294.1)
K [auth L]	Pribosyltran	e4lajL1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Pribosyltran	ECOD (v294.1)
J [auth M]	Pribosyltran	e4lajM1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Pribosyltran	ECOD (v294.1)
I [auth H]	Pribosyltran	e4lajH1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Pribosyltran	ECOD (v294.1)
H [auth C]	Pribosyltran	e4lajC1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Pribosyltran	ECOD (v294.1)
G	Pribosyltran	e4lajG1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Pribosyltran	ECOD (v294.1)
F [auth D]	Pribosyltran	e4lajD1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Pribosyltran	ECOD (v294.1)
E [auth K]	Asp	e4lajK1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: Asp	ECOD (v294.1)
D [auth B]	AWS	e4lajB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: AWS	ECOD (v294.1)
C [auth A]	AWS	e4lajA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: AWS	ECOD (v294.1)
B [auth F]	AWS	e4lajF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: AWS	ECOD (v294.1)
A [auth J]	AWS	e4lajJ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: AWS	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth B]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (4.3.0)
C [auth A]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (4.3.0)
B [auth F]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (4.3.0)
A [auth J]	2.170.40.20	Mainly Beta	Beta Complex	HIV Envelope Protein Gp120	Chain G	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
I [auth H], J [auth M], K [auth L], L [auth I]	miniprotein M48U1 (Protein)	VH	Lama glama (llama)	IGHV3S101, IGHJ401	V-DOMAIN VH	IG	(VH-CH1)_L-KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
I [auth H], J [auth M], K [auth L], L [auth I]	Heavy Chain	IGHV1	-	hiv-1 yu2 gp120 envelope glycoprotein \| cd4-mimetic miniprotein m48u1	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth H], J [auth M], K [auth L], L [auth I]	Llama single domain antibody, JM4	-	response to stimulus immune response immune system process adaptive immune response	protein-containing complex immunoglobulin complex cellular anatomical structure extracellular region
E [auth K], F [auth D], G, H [auth C]	CD4-mimetic miniprotein M48U1	-	-	-
A [auth J], B [auth F], C [auth A], D [auth B]	HIV-1 YU2 gp120 envelope glycoprotein	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth H], J [auth M], K [auth L], L [auth I]	IPR050199	Immunoglobulin Heavy Variable	Family
I [auth H], J [auth M], K [auth L], L [auth I]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
I [auth H], J [auth M], K [auth L], L [auth I]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
I [auth H], J [auth M], K [auth L], L [auth I]	IPR013106	Immunoglobulin V-set domain	Domain
I [auth H], J [auth M], K [auth L], L [auth I]	IPR003599	Immunoglobulin domain subtype	Domain
I [auth H], J [auth M], K [auth L], L [auth I]	IPR007110	Immunoglobulin-like domain	Domain
A [auth J], B [auth F], C [auth A], D [auth B]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth J], B [auth F], C [auth A], D [auth B]	IPR036377	Gp120 core superfamily	Homologous Superfamily
A [auth J], B [auth F], C [auth A], D [auth B]	IPR000328	Retroviral envelope protein GP41-like	Domain
A [auth J], B [auth F], C [auth A], D [auth B]	IPR037527	Envelope glycoprotein Gp160	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth K], F [auth D], G, H [auth C]	DPR
E [auth K], F [auth D], G, H [auth C]	MPT
E [auth K], F [auth D], G, H [auth C]	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109
E [auth K], F [auth D], G, H [auth C]	U2X	Parent Component: TYR RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100

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.