4NM8 | pdb_00004nm8

Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
K [auth N]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
I [auth M]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
G [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8088048	3001616	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8094281	3001342	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	e4nm8H3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: V-set	F:	ECOD (20:10:01)
J [auth I]	e4nm8I1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)
L [auth J]	e4nm8J1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)
K [auth N]	e4nm8N1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)
I [auth M]	e4nm8M1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)
G [auth L]	e4nm8L1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)
A	e4nm8A1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: EF-hand_1, EF-hand_7	F:	ECOD (20:10:01)
C	e4nm8C1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)
E	e4nm8E1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: OMPdecase	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
D	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
F	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (4.3.0)
A	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
C	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
E	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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, J [auth I], L [auth J]	CR8043 Fab	VH-CH1	Homo sapiens (human)	IGHV1-301, IGHJ401, IGHJ402, IGHJ403, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)
G [auth L], I [auth M], K [auth N]	CR8043 Fab	L-KAPPA	Homo sapiens (human)	IGKV4-101, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202609-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
H, J [auth I], L [auth J]	Heavy Chain	IGHV1	-	hemagglutinin ha2 chain \| hemagglutinin ha1 chain	SAbDab (2026-03-13)
G [auth L], I [auth M], K [auth N]	Light Chain	IGKV4	Kappa	hemagglutinin ha2 chain \| hemagglutinin ha1 chain	SAbDab (2026-03-13)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth L], I [auth M], K [auth N]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H, J [auth I], L [auth J]	Antibody CR8043, Heavy Chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
G [auth L], I [auth M], K [auth N]	Antibody CR8043, Light Chain	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex
B, D, F	Hemagglutinin HA2 Chain	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 Chain	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
H, J [auth I], L [auth J]	IPR003597	Immunoglobulin C1-set	Domain
H, J [auth I], L [auth J]	IPR050199	Immunoglobulin Heavy Variable	Family
H, J [auth I], L [auth J]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
H, J [auth I], L [auth J]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
H, J [auth I], L [auth J]	IPR013106	Immunoglobulin V-set domain	Domain
H, J [auth I], L [auth J]	IPR003599	Immunoglobulin domain subtype	Domain
H, J [auth I], L [auth J]	IPR007110	Immunoglobulin-like domain	Domain
H, J [auth I], L [auth J]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
G [auth L], I [auth M], K [auth N]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth L], I [auth M], K [auth N]	IPR050380	Immune Recognition and Response Modulators	Family
G [auth L], I [auth M], K [auth N]	IPR003597	Immunoglobulin C1-set	Domain
G [auth L], I [auth M], K [auth N]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
G [auth L], I [auth M], K [auth N]	IPR007110	Immunoglobulin-like domain	Domain
G [auth L], I [auth M], K [auth N]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth L], I [auth M], K [auth N]	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency