6WXL | pdb_00006wxl

Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 HA trimer

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
I [auth J]	d6wxlj_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth E]	d6wxle_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth L]	d6wxll_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H [auth I]	d6wxli_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/Shanghai/JS01/2013(H7N9)) ) [TaxId: 1395980 ],	SCOPe (2.08)
E [auth D]	d6wxld_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/Shanghai/JS01/2013(H7N9)) ) [TaxId: 1395980 ],	SCOPe (2.08)
B	d6wxlb_	Coiled coil proteins	Stalk segment of viral fusion proteins	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	Influenza hemagglutinin (stalk)	(Influenza A virus (A/Shanghai/JS01/2013(H7N9)) ) [TaxId: 1395980 ],	SCOPe (2.08)
L [auth G]	d6wxlg_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/JS01/2013(H7N9)) ) [TaxId: 1395980 ],	SCOPe (2.08)
K [auth C]	d6wxlc_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/JS01/2013(H7N9)) ) [TaxId: 1395980 ],	SCOPe (2.08)
A	d6wxla_	All beta proteins	Viral protein domain	Viral protein domain	automated matches	automated matches	(Influenza A virus (A/Shanghai/JS01/2013(H7N9)) ) [TaxId: 1395980 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth G]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8103232	3001342	SCOP2B (2022-06-29)
K [auth C]	SCOP2B Superfamily	Influenza hemagglutinin domain-like	8103232	3001342	SCOP2B (2022-06-29)
A	SCOP2 Family	Influenza hemagglutinin headpiece	8103231	4002506	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Influenza hemagglutinin domain-like	8103232	3001342	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)
J [auth K]	V-set_8	e6wxlK1	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 F]	V-set_8	e6wxlF1	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)
D [auth H]	V-set_8	e6wxlH1	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)
I [auth J]	V-set	e6wxlJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F [auth E]	V-set	e6wxlE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C [auth L]	V-set	e6wxlL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
H [auth I]	Hemagglutinin_2nd	e6wxlI1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: Hemagglutinin_2nd	ECOD (1.6)
E [auth D]	Hemagglutinin_2nd	e6wxlD1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: Hemagglutinin_2nd	ECOD (1.6)
B	Hemagglutinin_2nd	e6wxlB1	A: alpha bundles	X: Hemagglutinin HA2 chain (From Topology)	H: Hemagglutinin HA2 chain (From Topology)	T: Hemagglutinin HA2 chain	F: Hemagglutinin_2nd	ECOD (1.6)
L [auth G]	Hemagglutinin_1st	e6wxlG1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
K [auth C]	Hemagglutinin_1st	e6wxlC1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)
A	Hemagglutinin_1st	e6wxlA1	A: beta sandwiches	X: jelly-roll	H: Viral protein domain (From Topology)	T: Viral protein domain	F: Hemagglutinin_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
G [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
I [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
H [auth I]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
E [auth D]	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)
B	3.90.20.10	Alpha Beta	Alpha-Beta Complex	Hemagglutinin Ectodomain	Chain B	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H], G [auth F], J [auth K]	Heavy Chain	IGHV1	-	hemagglutinin ha2 chain \| hemagglutinin ha1 chain	SAbDab (2025-11-28)
C [auth L], F [auth E], I [auth J]	Light Chain	IGKV2	Kappa	hemagglutinin ha2 chain \| hemagglutinin ha1 chain	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, K [auth C], L [auth G]	PF00509	Haemagglutinin (Hemagglutinin)	Haemagglutinin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth H], G [auth F], J [auth K]	1D21 Heavy chain	-	-	-
C [auth L], F [auth E], I [auth J]	1D12 Light chain	-	-	-
B, E [auth D], H [auth I]	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, K [auth C], L [auth G]	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
B, E [auth D], H [auth I]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
B, E [auth D], H [auth I]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
B, E [auth D], H [auth I]	IPR000149	Haemagglutinin, influenzavirus A	Family
B, E [auth D], H [auth I]	IPR013828	Haemagglutinin, HA1 chain, alpha/beta domain superfamily	Homologous Superfamily
A, K [auth C], L [auth G]	IPR001364	Haemagglutinin, influenzavirus A/B	Family
A, K [auth C], L [auth G]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A, K [auth C], L [auth G]	IPR000149	Haemagglutinin, influenzavirus A	Family
A, K [auth C], L [auth G]	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.