3GBM

Crystal Structure of Fab CR6261 in Complex with a H5N1 influenza virus hemagglutinin.

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
Thera-SAbDab Antibody Annotation
Protein Family 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	d3gbma1	All beta proteins	Viral protein domain	Viral protein domain	Influenza hemagglutinin headpiece	Hemagglutinin	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
A	d3gbma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
C	d3gbmc1	All beta proteins	Viral protein domain	Viral protein domain	Influenza hemagglutinin headpiece	Hemagglutinin	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
C	d3gbmc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
B	d3gbmb1	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
B	d3gbmb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
D	d3gbmd_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	A/Viet Nam/1203/2004(H5N1) (Influenza A virus (A/Viet Nam/1203/2004(H5N1)) ) [TaxId: 284218 ],	SCOPe (2.08)
E [auth H]	d3gbmh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G [auth I]	d3gbmi_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d3gbml2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth L]	d3gbml1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth M]	d3gbmm2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth M]	d3gbmm1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Influenza hemagglutinin (stalk)	8087922	3001616	SCOP2B (2022-06-29)
D	SCOP2 Family	Influenza hemagglutinin (stalk)	8087921	4003840	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Influenza hemagglutinin (stalk)	8087922	3001616	SCOP2 (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	Hemagglutinin_1st	e3gbmA1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
C	Hemagglutinin_1st	e3gbmC1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
E [auth H]	V-set_8	e3gbmH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth H]	C1-set_1	e3gbmH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
G [auth I]	V-set_8	e3gbmI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
G [auth I]	C1-set_1	e3gbmI2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F [auth L]	C1-set	e3gbmL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
F [auth L]	V-set_3	e3gbmL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
H [auth M]	C1-set	e3gbmM2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)

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	2.10.77.10	Mainly Beta	Ribbon	Hemagglutinin	Chain A, domain 2	CATH (4.3.0)
C	3.90.209.20	Alpha Beta	Alpha-Beta Complex	Hemagglutinin (Ha1 Chain)	Chain: A	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)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth M]	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
E [auth H], G [auth I]	Fab CR6261	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6906, IGHV1-6912, IGHV1-6913, IGHV1-6914, IGHV1-69D01, IGHJ603, IGHJ604, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202450-0)
F [auth L], H [auth M]	Fab CR6261	L-LAMBDA	Homo sapiens (human)	IGLV1-5101, IGLJ201, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202450-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth H], G [auth I]	Heavy Chain	IGHV1	-	hemagglutinin \| hemagglutinin	SAbDab (2024-12-20)
F [auth L], H [auth M]	Light Chain	IGLV1	Lambda	hemagglutinin \| hemagglutinin	SAbDab (2024-12-20)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
E [auth H], G [auth I]	Diridavumab	Influenza A HA2	Therapeutic SAbDab (2024-12-20)
F [auth L], H [auth M]	Diridavumab	Influenza A HA2	Therapeutic SAbDab (2024-12-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family
B, D	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Hemagglutinin	identical protein binding protein binding 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 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	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane
B, D	Hemagglutinin	identical protein binding protein binding 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 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	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane
E [auth H], G [auth I]	antibody (Fab)	-	-	-
F [auth L], H [auth M]	antibody (Fab)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, C	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, C	IPR000149	Haemagglutinin, influenzavirus A	Family
A, C	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
B, D	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B, D	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B, D	IPR000149	Haemagglutinin, influenzavirus A	Family
B, D	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.