2Q8B | pdb_00002q8b

Structure of the malaria antigen AMA1 in complex with a growth-inhibitory antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth H]	d2q8bh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth L]	d2q8bl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth L]	d2q8bl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth H]	V-set_8	e2q8bH2	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)
C [auth H]	C1-set_1	e2q8bH1	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)
B [auth L]	C1-set_4	e2q8bL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e2q8bL1	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)
A	AMA-1_1st	e2q8bA2	A: few secondary structure elements	X: Hairpin loop containing domain-like (From Topology)	H: Hairpin loop containing domain-like (From Topology)	T: Hairpin loop containing domain-like	F: AMA-1_1st	ECOD (1.6)
A	AMA-1_2nd	e2q8bA1	A: few secondary structure elements	X: Hairpin loop containing domain-like (From Topology)	H: Hairpin loop containing domain-like (From Topology)	T: Hairpin loop containing domain-like	F: AMA-1_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	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 H]	1F9	VH-CH1	Mus musculus (house mouse)	IGHV14-302, IGHJ201, IGHG2B*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202549-0)
B [auth L]	1F9	L-KAPPA	Mus musculus (house mouse)	IGKV6-3201, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202549-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV14	-	apical membrane antigen 1	SAbDab (2025-12-19)
B [auth L]	Light Chain	IGKV6	Kappa	apical membrane antigen 1	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A	PF02430	Apical membrane antigen 1 (AMA-1)	Apical membrane antigen 1	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth H]	1F9 heavy chain	binding antigen binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination cellular process phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination positive regulation of acute inflammatory response to antigenic stimulus regulation of immune effector process regulation of acute inflammatory response to antigenic stimulus positive regulation of leukocyte mediated immunity inflammatory response to antigenic stimulus positive regulation of hypersensitivity positive regulation of inflammatory response positive regulation of adaptive immune response positive regulation of immunoglobulin mediated immune response hypersensitivity regulation of adaptive immune response response to external stimulus regulation of inflammatory response regulation of B cell mediated immunity regulation of leukocyte mediated immunity positive regulation of defense response regulation of acute inflammatory response inflammatory response positive regulation of type I hypersensitivity regulation of type I hypersensitivity regulation of defense response regulation of response to external stimulus positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of acute inflammatory response positive regulation of B cell mediated immunity type I hypersensitivity positive regulation of response to external stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stress regulation of response to stress regulation of immunoglobulin mediated immune response positive regulation of immune effector process acute inflammatory response regulation of hypersensitivity defense response regulation of inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus regulation of lymphocyte mediated immunity regulation of myeloid leukocyte mediated immunity regulation of type IIa hypersensitivity myeloid leukocyte mediated immunity regulation of type II hypersensitivity type II hypersensitivity positive regulation of myeloid leukocyte mediated immunity type IIa hypersensitivity positive regulation of type IIa hypersensitivity positive regulation of type II hypersensitivity humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway activation of immune response regulation of localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization positive regulation of endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport phagocytosis, recognition cell recognition	protein-containing complex cellular anatomical structure extracellular region extracellular space immunoglobulin complex, circulating immunoglobulin complex cell periphery plasma membrane membrane
B [auth L]	1F9 light chain	-	-	-
A	Apical membrane antigen 1	-	biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
C [auth H]	IPR003597	Immunoglobulin C1-set	Domain
C [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth H]	IPR007110	Immunoglobulin-like domain	Domain
C [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A	IPR024056	Apical membrane antigen 1 domain superfamily	Homologous Superfamily
A	IPR003298	Apical membrane antigen 1	Family

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.