9TJX: Factor VII Gla domain

Structure of factor VII Gla domain bound to EPCR. Determined by X-ray diffraction at 3.0 Å resolution. Released 25 Mar 2026.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 6,759
Mol. weight: 112.05 kDa
Ligands: CA, NAG, PTY, MG
Released: 25 Mar 2026

Explore 9TJX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9TJX contains 47 α-helices and 32 β-strands across 8 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-21	13	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	93-103	11	1
α-helix	109-110	2
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	156-160	5
α-helix	161-163	3
α-helix	164-168	5
α-helix	169-176	8

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	9-21	13	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	93-103	11	2
α-helix	109-110	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	156-160	5
α-helix	161-163	3
α-helix	164-169	6
α-helix	170-176	7

Chain C: 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	94-102	9	3
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	155	1
α-helix	156-160	5
α-helix	161-163	3
α-helix	164-169	6
α-helix	170-176	7

Chain D: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-21	11	4
β-strand	24-33	10	4
β-strand	36-44	9	4
β-strand	49-52	4	4
α-helix	59-87	29
β-strand	93-102	10	4
β-strand	111-118	8	4
β-strand	121-127	7	4
β-strand	132-135	4	4
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

Chains E, F, L and R: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	6-8	3
α-helix	10-11	2
α-helix	13	1
α-helix	14-18	5
α-helix	24-30	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endothelial protein C receptor	A, B, C, D	protein	195	Homo sapiens	Q9UNN8 (AlphaFold model)
Factor VII light chain	E, F, L, R	protein	32	Homo sapiens	P08709 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9TJX_1 Endothelial protein C receptor (chains A, B, C, D)
GPSQDASDGLQRLHMLQISYFRDPYHVWYQGQASLGGHLTHVLEGPDTNTTIIQLQPLQE
PESWARTQSGLQSYLLQFHGLVRLVHQERTLAFPLTIRCFLGCELPPEGSRAHVFFEVAV
NGSSFVSFRPERALWQADTQVTSGVVTFTLQQLNAYNRTRYELREFLEDTCVQYVQKHIS
AENTKGSQTSRSYTS

Sequence of entity 2 (E, F, L, R), FASTA

>9TJX_2 Factor VII light chain (chains E, F, L, R)
ANAFLEELRPGSLERECKEEQCSFEEAREIFK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	20
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
PTY	Phosphatidylethanolamine	C40 H80 N O8 P	4
MG	Magnesium ion	Mg	7

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Structure of factor VII Gla domain bound to EPCR. Lopez-Sagaseta, J., Dichiara-Rodriguez, M.G. Blood Adv (2026) 10:3431-3434. DOI 10.1182/bloodadvances.2026019642 · 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
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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