5UK2 | pdb_00005uk2

CryoEM structure of an influenza virus receptor-binding site antibody-antigen interface - Class 4

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT 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)
F	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087960	3001616	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087960	3001616	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087960	3001616	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087762	3001342	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087762	3001342	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087762	3001342	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	Plexin_RBD	e5uk2I1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
H	Plexin_RBD	e5uk2H1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
G	Plexin_RBD	e5uk2G1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
F	Plexin_RBD	e5uk2F1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
D	Plexin_RBD	e5uk2D1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
B	Plexin_RBD	e5uk2B1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
E	Plexin_RBD	e5uk2E1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
C	Plexin_RBD	e5uk2C1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)
A	Plexin_RBD	e5uk2A1	A: alpha bundles	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Plexin_RBD	ECOD (develop294)

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
G, H, I	scFv K1915	SCFV-KAPPA-HEAVY	Homo sapiens (human)	IGKV3-2001, IGKJ401, IGKJ402, IGHV3-1301, IGHV3-1304, IGHJ101, IGHJ401, IGHJ501, IGHJ502, IGHJ402, IGHJ4*03	V-DOMAIN V-KAPPA, V-DOMAIN VH	IG	SCFV-KAPPA-HEAVY	IMGT (202610-0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I	scFv	-	-	-
B, D, F	Hemagglutinin HA2	host cell surface binding binding host cell surface receptor binding	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 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 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 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 non-lytic viral release viral budding virion assembly exit from host cell viral budding from plasma membrane viral release from host cell import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization 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	cellular anatomical structure membrane virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part
A, C, E	Hemagglutinin HA1	host cell surface binding binding host cell surface receptor binding	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 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 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 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 non-lytic viral release viral budding virion assembly exit from host cell viral budding from plasma membrane viral release from host cell import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization 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	cellular anatomical structure membrane virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B, D, F	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B, D, F	IPR000149	Haemagglutinin, influenzavirus A	Family
B, D, F	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
A, C, E	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, C, E	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, C, E	IPR000149	Haemagglutinin, influenzavirus A	Family
A, C, E	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.