9P0X

Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted)

Summary for 9P0X

• Entry DOI: 10.2210/pdb9p0x/pdb
• EMDB information: 71090
• Descriptor: Factor VII light chain, beta-D-glucopyranose, alpha-L-fucopyranose, ... (11 entities in total)
• Functional Keywords: complex, nanodisc, blood clotting
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 7
• Total formula weight: 184268.60

Authors

Photenhauer, A.L.,Sedzro, J.C.,Ohi, M.D.,Morrissey, J.H. (deposition date: 2025-06-07, release date: 2025-08-27)

Primary citation

Sedzro, J.C.,Photenhauer, A.L.,Birkle, F.,Meze, K.,Mortenson, A.,Duckworth, C.,Wen, P.C.,Kearns, S.,Cianfrocco, M.A.,Tajkhorshid, E.,Ohi, M.D.,Morrissey, J.H.
Cryo-EM structure of the tissue factor/factor VIIa complex with a factor X mimetic reveals a novel allosteric mechanism.
Blood, 2025

PubMed Abstract: Blood clotting is triggered in hemostasis and thrombosis when the membrane-bound tissue factor (TF)/factor VIIa (FVIIa) complex activates factor X (FX). There are no structures of TF/FVIIa on membranes, with or without FX. Using cryo-EM to address this gap, we assembled TF/FVIIa complexes on nanoscale membrane bilayers (nanodiscs), bound to XK1 and an antibody fragment. XK1 is a FX mimetic whose protease domain is replaced by the first Kunitz-type (K1) domain of tissue factor pathway inhibitor, while 10H10 is a non-inhibitory, anti-TF antibody. We determined a cryo-EM structure of a TF/FVIIa/XK1/10H10/nanodisc complex with a resolution of 3.7 Å, allowing us to model all the protein backbones. TF/FVIIa extends perpendicularly from the membrane, interacting with a "handle shaped" XK1 at two locations: the K1 domain docks into FVIIa's active site, while the γ-carboxyglutamate-rich (GLA) domain binds to TF's substrate-binding exosite. The FX and FVIIa GLA domains also contact each other and the membrane surface. Except for a minor contact between the first epidermal growth factor (EGF)-like domain of XK1 and TF, the rest of the FX light chain does not interact with TF/FVIIa. The structure reveals a previously unrecognized, membrane-dependent allosteric activation mechanism between FVIIa and TF where a serine-rich loop in TF that partially obscures the TF exosite must undergo a shift to allow access of the FX GLA domain to its final binding location on the membrane-bound TF/FVIIa complex. This mechanism also provides a novel explanation for the otherwise puzzling phenomenon of TF encryption/decryption on cell surfaces.

PubMed: 40811856
DOI: 10.1182/blood.2025029430

Experimental method

ELECTRON MICROSCOPY (3.7 Å)