2YK0

Structure of the N-terminal NTS-DBL1-alpha and CIDR-gamma double domain of the PfEMP1 protein from Plasmodium falciparum varO strain.


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AEUF07604e2yk0A1 A: beta meandersX: Beta meander domain in PfEMP1 protein (From Topology)H: Beta meander domain in PfEMP1 protein (From Topology)T: Beta meander domain in PfEMP1 proteinF: EUF07604ECOD (1.6)
ADuffy_bindinge2yk0A2 A: alpha bundlesX: 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 subdomainF: Duffy_bindingECOD (1.6)
APFEMPe2yk0A4 A: alpha bundlesX: 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 subdomainF: PFEMPECOD (1.6)
APTZ00176_1e2yk0A3 A: alpha bundlesX: 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 subdomainF: PTZ00176_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A1.20.58.1930 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF03011PFEMP1 DBL domain (PFEMP)PFEMP1 DBL domainPfEMP1 (Plasmodium falciparum erythrocyte membrane protein) has been identified as the rosetting ligand of the malaria parasite P. falciparum [1,2]. Rosetting is the adhesion of infected erythrocytes with uninfected erythrocytes in the vasculature ...PfEMP1 (Plasmodium falciparum erythrocyte membrane protein) has been identified as the rosetting ligand of the malaria parasite P. falciparum [1,2]. Rosetting is the adhesion of infected erythrocytes with uninfected erythrocytes in the vasculature of the infected organ, and is associated with severe malaria. PfEMP1 interacts with Complement Receptor One on uninfected erythrocytes to form rosettes [2]. The extreme variation within these proteins and the grouping of var genes implies that var gene recombination preferentially occurs within var gene groups. These groups reflect a functional diversification that has evolved to cope with the varying conditions of transmission and host immune response met by the parasite [3]. A recombination hotspot was uncovered between Duffy-binding-like (DBL) subdomains [4]. Solution of the crystal structure of the N-terminal and first DBL region of PfEMP1 from the VarO variant of the PfEMP1 protein is found to be directly implicated in rosetting as the heparin-binding site [5].
Domain
PF18562Cysteine-Rich Interdomain Region 1 gamma (CIDR1_gamma)Cysteine-Rich Interdomain Region 1 gammaRosetting is the capacity of infected RBCs to bind uninfected RBCs, which is consistently associated with severe malaria in African children. The rosette-forming PfEMP1 adhesins, namely IT4/R29, Palo Alto 89F5 VarO, 3D7/PF13_0003 and IT4/var60, belon ...Rosetting is the capacity of infected RBCs to bind uninfected RBCs, which is consistently associated with severe malaria in African children. The rosette-forming PfEMP1 adhesins, namely IT4/R29, Palo Alto 89F5 VarO, 3D7/PF13_0003 and IT4/var60, belong to a specific sub-group called groupA/UpsA var genes and all four present a specific Duffy Binding-Like and and Cysteine-Rich Interdomain Region (DBL1alpha1-CIDR1gamma) double domain Head region found at the extracellular region of PfEMP1. This entry represents the CIDR1gamma domain which increases the binding affinity to VarO (Palo Alto VarO parasites) [1-2].
Domain
PF05424Duffy binding domain (Duffy_binding)Duffy binding domain- Family
PF15447N-terminal segments of PfEMP1 (NTS)N-terminal segments of PfEMP1This 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