6SNY: Synthetic mimic of an EPCR-binding PfEMP1

Synthetic mimic of an EPCR-binding PfEMP1 bound to EPCR. Determined by X-ray diffraction at 3.11 Å resolution. Released 4 Sept 2019.

Method: X-ray diffraction
Resolution: 3.11 Å
Organisms: synthetic construct, Homo sapiens
Chains: 3
Atoms: 4,015
Mol. weight: 64.1 kDa
Ligands: PTY, NAG
Released: 4 Sept 2019

Explore 6SNY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SNY contains 15 α-helices and 16 β-strands across 3 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	2-30	29
α-helix	51-77	27
α-helix	79-83	5
α-helix	90-118	29

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	1
β-strand	24-33	10	1
β-strand	36-44	9	1
β-strand	49-52	4	1
α-helix	59-87	29
β-strand	93-102	10	1
β-strand	111-118	8	1
β-strand	121-127	7	1
β-strand	132-135	4	1
α-helix	142-151	10
α-helix	159-163	5
α-helix	164-169	6
α-helix	170-176	7

Chain C: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	10-21	12	2
β-strand	24-33	10	2
β-strand	36-44	9	2
β-strand	49-52	4	2
α-helix	59-87	29
β-strand	93-102	10	2
β-strand	111-118	8	2
β-strand	121-127	7	2
β-strand	132-135	4	2
α-helix	142-151	10
α-helix	155-157	3
α-helix	159-163	5
α-helix	164-169	6
α-helix	170-176	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synthetic EPCR binding protein	A	protein	124	synthetic construct
Endothelial protein C receptor	B, C	protein	193	Homo sapiens	Q9UNN8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SNY_1 Synthetic EPCR binding protein (chains A)
NNWEQQKKNIEDDLDRYKKRAEELRKEAEKARKEARKTEDPTEEAKKEWEKRCKELEERA
RKLEDEAKDRVNDLFDSNFFQVIYSGDNDEEEWKKEKDRAEKEIEEWFKRIKEKCEEIKK
RLEQ

Sequence of entity 2 (B, C), FASTA

>6SNY_2 Endothelial protein C receptor (chains B, C)
SQDASDGLQRLHMLQISYFRDPYHVWYQGNASLGGHLTHVLEGPDTNTTIIQLQPLQEPE
SWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAVNG
SSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHISAE
NTKGSQTSRSYTS

Ligands and cofactors

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

Primary citation

Structure-Guided Design of a Synthetic Mimic of an Endothelial Protein C Receptor-Binding PfEMP1 Protein. Barber, N.M., Lau, C.K.Y., Turner, L. et al. mSphere (2021) 6. DOI 10.1128/mSphere.01081-20 · 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
4V3D 2.65 Å, The CIDRa domain from HB3var03 PfEMP1 bound to endothelial protein C receptor
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
8C44 3.2 Å, HB3VAR03 apo headstructure (PfEMP1 A) complexed with EPCR

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