8RLD

SPNS2:sfGFP hetero dimer assembled by Di-Gluebody - SPNS2 local refinement

Summary for 8RLD

• Entry DOI: 10.2210/pdb8rld/pdb
• EMDB information: 19339
• Descriptor: Sphingosine-1-phosphate transporter SPNS2, DODECYL-BETA-D-MALTOSIDE (2 entities in total)
• Functional Keywords: dna helicase, di-gluebody, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 59472.83

Authors

Yi, G.,Ye, M.,Mamalis, D.,Sauer, D.B.,von Delft, F.,Davis, B.G.,Gilbert, R.J.C. (deposition date: 2024-01-02, release date: 2025-01-15, Last modification date: 2026-01-07)

Primary citation

Yi, G.,Mamalis, D.,Ye, M.,Carrique, L.,Fairhead, M.,Li, H.,Duerr, K.L.,Zhang, P.,Sauer, D.B.,von Delft, F.,Davis, B.G.,Gilbert, R.J.C.
Covalently constrained 'Di-Gembodies' enable parallel structure solutions by cryo-EM.
Nat.Chem.Biol., 22:69-76, 2026

PubMed Abstract: Whilst cryo-electron microscopy(cryo-EM) has become a routine methodology in structural biology, obtaining high-resolution cryo-EM structures of small proteins (<100 kDa) and increasing overall throughput remain challenging. One approach to augment protein size and improve particle alignment involves the use of binding proteins or protein-based scaffolds. However, a given imaging scaffold or linking module may prove inadequate for structure solution and availability of such scaffolds remains limited. Here, we describe a strategy that exploits covalent dimerization of nanobodies to trap an engineered, predisposed nanobody-to-nanobody interface, giving Di-Gembodies as modular constructs created in homomeric and heteromeric forms. By exploiting side-chain-to-side-chain assembly, they can simultaneously display two copies of the same or two distinct proteins through a subunit interface that provides sufficient constraint required for cryo-EM structure determination. We validate this method with multiple soluble and membrane structural targets, down to 14 kDa, demonstrating a flexible and scalable platform for expanded protein structure determination.

PubMed: 40817135
DOI: 10.1038/s41589-025-01972-7

Experimental method

ELECTRON MICROSCOPY (2.84 Å)