2XU0 | pdb_00002xu0

Crystal structure of the NTS-DBL1(alpha-1) domain of the Plasmodium falciparum membrane protein 1 (PfEMP1) from the varO strain.

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Duffy_binding	e2xu0A1	A: alpha bundles	X: Duffy-binding-like domain, N-terminal subdomain (From Topology)	H: Duffy-binding-like domain, N-terminal subdomain (From Topology)	T: Duffy-binding-like domain, N-terminal subdomain	F: Duffy_binding	ECOD (1.6)
A	PTZ00176_1	e2xu0A2	A: alpha bundles	X: Duffy-binding-like domain, C-terminal subdomain (From Topology)	H: Duffy-binding-like domain, C-terminal subdomain (From Topology)	T: Duffy-binding-like domain, C-terminal subdomain	F: PTZ00176_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22672	Duffy-binding-like domain, C-terminal subdomain (DBL_C)	Duffy-binding-like domain, C-terminal subdomain	This entry represents a domain found C-terminally to Duffy binding-like (DBL) domains of PfEMP1, the adhesin of Plasmodium falciparum which is an important target for protective immunity and is implicated in the pathology of malaria through its abili ...	This entry represents a domain found C-terminally to Duffy binding-like (DBL) domains of PfEMP1, the adhesin of Plasmodium falciparum which is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors [1-5]. This domain consists of an helical bundle.	Domain
A	PF05424	Duffy binding domain (Duffy_binding)	Duffy binding domain	-	Family
A	PF15447	N-terminal segments of PfEMP1 (NTS)	N-terminal segments of PfEMP1	This family, the N-terminal segment, is the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1) proteins. PfEMP1 is an important target for protective immunity and is implicat ...	This family, the N-terminal segment, is the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1) proteins. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors [1]. A structural and functional study of the N-terminal domain of PfEMP1 from the VarO variant comprising the N-terminal segment (NTS) and the first DBL domain (DBL1alpha1), shows this region is directly implicated in rosetting. NTS, previously thought to be a structurally independent component of PfEMP1, forms an integral part of the DBL1alpha domain that is found to be the important heparin-binding site [2]. This family is closely associated with PFEMP, Pfam:PF03011, and Duffy_binding, Pfam:PF05424.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ERYTHROCYTE MEMBRANE PROTEIN 1	cation binding ion binding binding metal ion binding small molecule binding host cell surface binding host cell surface receptor binding	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008602	Duffy-antigen binding domain	Domain
A	IPR004258	Duffy-binding-like domain	Domain
A	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A	IPR042202	Duffy-antigen binding superfamily	Homologous Superfamily
A	IPR029211	Plasmodium falciparum erythrocyte membrane protein 1, acidic terminal segment	Domain
A	IPR029210	Plasmodium falciparum erythrocyte membrane protein-1, N-terminal segment	Domain
A	IPR041480	Cysteine-rich interdomain region 1 gamma	Domain
A	IPR054595	Duffy-binding-like domain, C-terminal subdomain	Domain

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	All alpha monotopic/peripheral	DBL (Duffy-binding like)	PfEMP1 (Plasmodium falciparum erythrocyte membrane protein)

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.