Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Covalently constrained 'Di-Gembodies' enable parallel structure solutions by cryo-EM.
Journal, issue, pages	Nat Chem Biol, Vol. 22, Issue 1, Page 69-76, Year 2026
Publish date	Aug 15, 2025
Authors	Gangshun Yi / Dimitrios Mamalis / Mingda Ye / Loic Carrique / Michael Fairhead / Huanyu Li / Katharina L Duerr / Peijun Zhang / David B Sauer / Frank von Delft / Benjamin G Davis / Robert J C Gilbert /
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.
External links	Nat Chem Biol / PubMed:40817135 / PubMed Central
Methods	EM (single particle)
Resolution	2.45 - 3.9 Å
Structure data	19331 8rl5 EMDB-19331, PDB-8rl5: DNA helicase RECQL5 in complex with homo Di-Gluebody G5-006 Method: EM (single particle) / Resolution: 3.79 Å 19332 8rl6 EMDB-19332, PDB-8rl6: DNA helicase RECQL5 in complex with homo Di-Gluebody G5-006 - RECQL5 local refinement Method: EM (single particle) / Resolution: 3.18 Å 19333 8rl7 EMDB-19333, PDB-8rl7: SPNS2 in complex with homo Di-Gluebody GbD12 Method: EM (single particle) / Resolution: 3.76 Å 19334 8rl8 EMDB-19334, PDB-8rl8: SPNS2 in complex with homo Di-Gluebody GbD12 - SPNS2 local refinement Method: EM (single particle) / Resolution: 2.79 Å 19335 8rl9 EMDB-19335, PDB-8rl9: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody Method: EM (single particle) / Resolution: 3.22 Å 19336 8rla EMDB-19336, PDB-8rla: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement Method: EM (single particle) / Resolution: 3.03 Å 19337 8rlb EMDB-19337, PDB-8rlb: RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - sfGFP local refinement Method: EM (single particle) / Resolution: 2.99 Å 19338 8rlc EMDB-19338, PDB-8rlc: SPNS2:sfGFP hetero dimer assembled by Di-Gluebody Method: EM (single particle) / Resolution: 3.9 Å 19339 8rld EMDB-19339, PDB-8rld: SPNS2:sfGFP hetero dimer assembled by Di-Gluebody - SPNS2 local refinement Method: EM (single particle) / Resolution: 2.84 Å 19340 8rle EMDB-19340, PDB-8rle: SPNS2:sfGFP hetero dimer assembled by Di-Gluebody - sfGFP local refinement Method: EM (single particle) / Resolution: 3.75 Å 50430 9fgv EMDB-50430, PDB-9fgv: Cryo-EM structure of MBP homo-dimer assembled by homo Di-Gluebody Method: EM (single particle) / Resolution: 3.39 Å 50432 9fgx EMDB-50432, PDB-9fgx: Cryo-EM structure of Lysozyme homo-dimer assembled by homo Di-Gluebody Method: EM (single particle) / Resolution: 3.53 Å 50433 9fgy EMDB-50433, PDB-9fgy: Cryo-EM structure of Lysozyme homo-dimer assembled by homo Di-Gluebody - Local refinement Method: EM (single particle) / Resolution: 3.16 Å 50525 9fkq EMDB-50525, PDB-9fkq: Cryo-EM structure of MBP homo-dimer assembled by homo Di-Gluebody - MBP local refinement Method: EM (single particle) / Resolution: 2.45 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-LMT: DODECYL-BETA-D-MALTOSIDE / detergentYM ChemComp-GOL*: GLYCEROL
Source	lama glama (llama) homo sapiens (human) aequorea victoria (jellyfish) escherichia coli (E. coli) gallus gallus (chicken)
Keywords	HYDROLASE / DNA helicase / Di-Gluebody / MEMBRANE PROTEIN / SPNS2 / GFP / RECQL5 / sfGFP / PROTEIN BINDING / Gluebody / Nanobody / cryo-EM SPA / small protein