5VK2 | pdb_00005vk2

Structural basis for antibody-mediated neutralization of Lassa virus

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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)
E [auth C]	SCOP2B Superfamily	Lassa virus GP1 subunit, receptor binding domain-like	8106407	3002852	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Lassa virus GP1 subunit, receptor binding domain-like	8106407	3002852	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lassa virus GP1 subunit, receptor binding domain-like	8106407	3002852	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)
E [auth C]	SBP_bac_8	e5vk2C1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
C [auth B]	Arena_glycoprot	e5vk2B1	A: alpha bundles	X: Envelope glycoprotein GP1	H: Envelope glycoprotein GP1	T: Envelope glycoprotein GP1	F: Arena_glycoprot	ECOD (develop294)
A	SBP_bac_8	e5vk2A1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
F [auth c]	PBP_like_2	e5vk2c1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: Beta domain of coronavirus spike glycoprotein	T: Beta domain of coronavirus spike glycoprotein	F: PBP_like_2	ECOD (develop294)
D [auth b]	PrpF	e5vk2b1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: Diaminopimelate epimerase-like	T: Diaminopimelate epimerase-like	F: PrpF	ECOD (develop294)
B [auth a]	PBP_like_2	e5vk2a1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: Beta domain of coronavirus spike glycoprotein	T: Beta domain of coronavirus spike glycoprotein	F: PBP_like_2	ECOD (develop294)
L	SBP_bac_8	e5vk2L1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
J [auth G]	SBP_bac_8	e5vk2G1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
H [auth E]	SBP_bac_8	e5vk2E1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
K [auth H]	SBP_bac_8	e5vk2H1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
I [auth F]	SBP_bac_8	e5vk2F1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)
G [auth D]	SBP_bac_8	e5vk2D1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: SBP_bac_8	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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
H [auth E], J [auth G], L	Fab 37.7H	L-LAMBDA	Homo sapiens (human)	IGLV2-2302, IGLJ302, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
G [auth D], I [auth F], K [auth H]	Fab 37.7H	VH-CH1	Homo sapiens (human)	IGHV3-2101, IGHV3-2102, IGHV3-2104, IGHV3-2103, IGHJ601, IGHG103, IGHG108, IGHG106	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H [auth E], J [auth G], L	Light Chain	IGLV2	Lambda	unknown \| pre-glycoprotein polyprotein gp complex	SAbDab (2026-03-20)
G [auth D], I [auth F], K [auth H]	Heavy Chain	IGHV3	-	unknown \| pre-glycoprotein polyprotein gp complex	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E [auth C]	Pre-glycoprotein polyprotein GP complex	cation binding ion binding binding metal ion binding small molecule binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host cellular process endocytosis involved in viral entry into host cell receptor-mediated endocytosis endocytosis	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane virion component viral membrane viral envelope membrane host cell plasma membrane virion membrane host cell Golgi membrane host cell Golgi apparatus
B [auth a], D [auth b], F [auth c]	Pre-glycoprotein polyprotein GP complex	cation binding ion binding binding metal ion binding small molecule binding	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell 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 import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell symbiont entry into host cellular process endocytosis involved in viral entry into host cell receptor-mediated endocytosis endocytosis	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane virion component viral membrane viral envelope membrane host cell plasma membrane virion membrane host cell Golgi membrane host cell Golgi apparatus
H [auth E], J [auth G], L	Fab 37.7H light chain	-	-	-
G [auth D], I [auth F], K [auth H]	Fab 37.7H heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C]	IPR043015	Arenavirus glycoprotein, zinc binding domain	Homologous Superfamily
A, C [auth B], E [auth C]	IPR001535	Arenavirus glycoprotein	Family
B [auth a], D [auth b], F [auth c]	IPR043015	Arenavirus glycoprotein, zinc binding domain	Homologous Superfamily
B [auth a], D [auth b], F [auth c]	IPR001535	Arenavirus glycoprotein	Family

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.