5GJS | pdb_00005gjs

Crystal structure of H1 hemagglutinin from A/California/04/2009 in complex with a neutralizing antibody 3E1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5gjsa1	All beta proteins	Viral protein domain	Viral protein domain	Influenza hemagglutinin headpiece	Hemagglutinin	(Influenza A virus (A/California/04/2009(H1N1)) ) [TaxId: 641501 ],	SCOPe (2.08)
A	d5gjsa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Influenza A virus (A/California/04/2009(H1N1)) ) [TaxId: 641501 ],	SCOPe (2.08)
C [auth L]	d5gjsl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d5gjsl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth H]	d5gjsh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth H]	d5gjsh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5gjsb_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	automated matches	automated matches	(Influenza A virus (A/California/04/2009(H1N1)) ) [TaxId: 641501 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087794	3001342	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087956	3001616	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)
A	Dynamin_N	e5gjsA1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: Dynamin_N	ECOD (develop294)
C [auth L]	Dynamin_N	e5gjsL1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: Dynamin_N	ECOD (develop294)
D [auth H]	Dynamin_N	e5gjsH1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: Dynamin_N	ECOD (develop294)
B	Dynamin_N	e5gjsB1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p)	T: Ribosomal protein L29 (L29p)	F: Dynamin_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
A	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	CATH (4.3.0)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth H]	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)

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
C [auth L]	Fab 3E1, neutralizing	L-KAPPA	Homo sapiens (human)	IGKV1-503, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
D [auth H]	Fab 3E1, neutralizing	VH-CH1	Homo sapiens (human)	IGHV4-407, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV1	Kappa	hemagglutinin \| hemagglutinin	SAbDab (2026-03-20)
D [auth H]	Heavy Chain	IGHV4	-	hemagglutinin \| hemagglutinin	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Hemagglutinin	cation binding ion binding binding metal ion binding small molecule binding host cell surface 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
C [auth L]	light chain of human neutralizing antibody 3E1	-	-	-
D [auth H]	heavy chain of human neutralizing antibody 3E1	-	-	-
B	Hemagglutinin	cation binding ion binding binding metal ion binding small molecule binding host cell surface 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
A	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A	IPR000149	Haemagglutinin, influenzavirus A	Family
A	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
B	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B	IPR000149	Haemagglutinin, influenzavirus A	Family
B	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.