6HJQ

Structure of Full-length Influenza Hemagglutinin (A/duck/Alberta/35/76) in complex with FISW84 Fab Fragment

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: mpstruc

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	8087728	3001342	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087728	3001342	SCOP2B (2022-06-29)
J [auth E]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8087728	3001342	SCOP2B (2022-06-29)
B	SCOP2 Family	Influenza hemagglutinin (stalk)	8087937	4003840	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Influenza hemagglutinin (stalk)	8087938	3001616	SCOP2 (2022-06-29)
K [auth D]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087938	3001616	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087938	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	PF00509	e6hjqA1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
I [auth C]	PF00509	e6hjqC1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
J [auth E]	PF00509	e6hjqE1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: PF00509	ECOD (1.6)
C [auth G]	PF07654	e6hjqG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth G]	PF07686	e6hjqG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth I]	PF07654	e6hjqI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth I]	PF07686	e6hjqI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth K]	PF07654	e6hjqK2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F [auth K]	PF07686	e6hjqK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth L]	PF07654	e6hjqL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H [auth L]	PF07686	e6hjqL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth H]	PF07654	e6hjqH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth H]	PF07686	e6hjqH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G [auth J]	PF07654	e6hjqJ2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G [auth J]	PF07686	e6hjqJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

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 G], E [auth I], F [auth K]	Fab FISW84	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHV3-23D01, IGHJ101, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
D [auth H], G [auth J], H [auth L]	Fab FISW84	L-KAPPA	Homo sapiens (human)	IGKV3-1501, IGKV3D-1501, IGKJ501, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth G], E [auth I], F [auth K]	Heavy Chain	IGHV3	-	hemagglutinin \| hemagglutinin	SAbDab (2024-04-26)
D [auth H], G [auth J], H [auth L]	Light Chain	IGKV3	Kappa	hemagglutinin \| hemagglutinin	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, I [auth C], J [auth E]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family
B, K [auth D], L [auth F]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, I [auth C], J [auth E]	Hemagglutinin	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 transport of virus	membrane cellular anatomical entity virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane
B, K [auth D], L [auth F]	Hemagglutinin	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 transport of virus	membrane cellular anatomical entity virion component virion membrane viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane
C [auth G], E [auth I], F [auth K]	Heavy chain of FISW84 Fab	-	-	-
D [auth H], G [auth J], H [auth L]	Light chain of FISW84 Fab	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, I [auth C], J [auth E]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, I [auth C], J [auth E]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, I [auth C], J [auth E]	IPR000149	Haemagglutinin, influenzavirus A	Family
A, I [auth C], J [auth E]	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
B, K [auth D], L [auth F]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B, K [auth D], L [auth F]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B, K [auth D], L [auth F]	IPR000149	Haemagglutinin, influenzavirus A	Family
B, K [auth D], L [auth F]	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, I [auth C], J [auth E], K [auth D] A, B, I [auth C], J [auth E], K [auth D], L [auth F]	OPM	Transmembrane	Bitopic proteins	Viral membrane fusion glycoprotein	Hemagglutinin

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, I [auth C], J [auth E], K [auth D] A, B, I [auth C], J [auth E], K [auth D], L [auth F]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, I [auth C], J [auth E], K [auth D] A, B, I [auth C], J [auth E], K [auth D], L [auth F]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Glycoproteins	Influenza Hemagglutinin, full length

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 R01GM133198.