4V3D: The CIDRa domain from HB3var03 PfEMP1

The CIDRa domain from HB3var03 PfEMP1 bound to endothelial protein C receptor. Determined by X-ray diffraction at 2.65 Å resolution. Released 17 Dec 2014.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: PLASMODIUM FALCIPARUM, HOMO SAPIENS
Chains: 4
Atoms: 6,397
Mol. weight: 102.89 kDa
Ligands: NAG, PTY
Released: 17 Dec 2014

Explore 4V3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4V3D contains 33 α-helices and 28 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	502-509	8	1
α-helix	518-521	4
α-helix	523-526	4
β-strand	537-544	8	1
β-strand	552-558	7	1
β-strand	567-570	4	1
α-helix	571-598	28
α-helix	607-630	24
α-helix	636-638	3
α-helix	641-643	3
β-strand	646	1	2
α-helix	647-653	7
α-helix	655-659	5
α-helix	665-682	18
β-strand	694	1	2
α-helix	695-714	20

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	3
β-strand	24-33	10	3
β-strand	36-44	9	3
β-strand	49-52	4	3
α-helix	59-87	29
β-strand	93-102	10	3
α-helix	109-110	2
β-strand	111-118	8	3
β-strand	121-127	7	3
β-strand	132-135	4	3
α-helix	142-151	10
α-helix	156-160	5
α-helix	161-163	3
α-helix	164-168	5
α-helix	169-176	8

Chain C: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	504-507	4	4
α-helix	518-521	4
α-helix	523-526	4
β-strand	539-542	4	4
β-strand	552-556	5	4
β-strand	568-570	3	4
α-helix	571-595	25
α-helix	607-630	24
α-helix	641-643	3
β-strand	646	1	5
α-helix	647-653	7
α-helix	655-659	5
α-helix	665-683	19
β-strand	694	1	5
α-helix	695-713	19

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	6
β-strand	24-33	10	6
β-strand	36-44	9	6
β-strand	49-52	4	6
α-helix	59-87	29
β-strand	93-102	10	6
α-helix	108-110	3
β-strand	111-118	8	6
β-strand	121-127	7	6
β-strand	132-135	4	6
α-helix	142-151	10
α-helix	156-160	5
α-helix	161-163	3
α-helix	164-168	5
α-helix	169-175	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HB3VAR03 cidra domain	A, C	protein	251	PLASMODIUM FALCIPARUM
Endothelial protein C receptor	B, D	protein	170	HOMO SAPIENS	Q9UNN8 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4V3D_1 HB3VAR03 CIDRA DOMAIN (chains A, C)
PDCGVECKNETCTPKTVIYPDCGKNEKYEPPGDAKNTEINVINSGDKEGYIFEKLSEFCT
NENNENGKNYEQWKCYYDNKKNNNKCKMEINIANSKLKNKVTSFDEFFDFWVRKLLIDTI
KWETELTYCINNTDVTDCNKCNKNCVCFDKWVKQKEDEWTNIMKLFTNKHDIPKKYYLNI
NDLFDSFFFQVIYKFNEGEAKWNELKENLKKQIASSKANNGTKDSEAAIKVLFNHIKEIA
TICKDNNTNEG

Sequence of entity 2 (B, D), FASTA

>4V3D_2 ENDOTHELIAL PROTEIN C RECEPTOR (chains B, D)
LQRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPESWARTQS
GLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNGSSFVSFR
PERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHI

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	2

Primary citation

Structural Conservation Despite Huge Sequence Diversity Allows Epcr Binding by the Pfemp1 Family Implicated in Severe Childhood Malaria. Lau, C.K.Y., Turner, L., Jespersen, J.S. et al. Cell Host Microbe (2015) 17:118. DOI 10.1016/J.CHOM.2014.11.007 · PubMed

Other PDB entries of the same protein (UniProt Q9UNN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1LQV 1.6 Å, Crystal structure of the Endothelial protein C receptor with phospholipid in the groove…
3JTC 1.6 Å, Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid…
7Q5D 1.8 Å, Structure of EPCR in a non-canonical conformation
7OKV 1.85 Å, Crystal structure of soluble EPCR after exposure to the nonionic surfactant Polysorbate 20
7OKS 1.95 Å, X-ray structure of soluble EPCR in P212121 space group
7OKT 1.95 Å, X-ray structure of soluble EPCR in C2221 space group
7OKU 1.95 Å, X-ray structure of soluble EPCR in P3121 space group
1L8J 2.0 Å, Crystal Structure of the Endothelial Protein C Receptor and Bound Phospholipid Molecule
4V3E 2.9 Å, The CIDRa domain from IT4var07 PfEMP1 bound to endothelial protein C receptor
9TJX 3.0 Å, Structure of factor VII Gla domain bound to EPCR
6SNY 3.11 Å, Synthetic mimic of an EPCR-binding PfEMP1 bound to EPCR
8C44 3.2 Å, HB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR

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