9IRV image
Deposition Date 2024-07-16
Release Date 2025-06-04
Last Version Date 2025-06-04
Entry Detail
PDB ID:
9IRV
Title:
MultiBody Refinement of dimeric DARPin and its bound GFP on a symmetric scaffold
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.47 Å
Aggregation State:
3D ARRAY
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DARPin
Chain IDs:A, B
Chain Length:394
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:Green fluorescent protein
Chain IDs:C
Chain Length:236
Number of Molecules:1
Biological Source:Aequorea victoria
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CRO C THR chromophore
Ligand Molecules
Primary Citation
A large, general and modular DARPin-apoferritin scaffold enables the visualization of small proteins by cryo-EM.
Iucrj 12 393 402 (2025)
PMID: 40277178 DOI: 10.1107/S2052252525003021

Abstact

Single-particle cryo-electron microscopy (cryo-EM) has emerged as an indispensable technique in structural biology that is pivotal for deciphering protein architectures. However, the medium-sized proteins (30-40 kDa) that are prevalent in both eukaryotic and prokaryotic organisms often elude the resolving capabilities of contemporary cryo-EM methods. To address this challenge, we engineered a scaffold strategy that securely anchors proteins of interest to a robust, symmetric base via a selective adapter. Our most efficacious constructs, namely models 4 and 6c, feature a designed ankyrin-repeat protein (DARPin) rigidly linked to an octahedral human apoferritin via a helical linker. By utilizing these large, highly symmetric scaffolds (∼1 MDa), we achieved near-atomic-resolution cryo-EM structures of green fluorescent protein (GFP) and maltose-binding protein (MBP), revealing nearly all side-chain densities of GFP and the distinct structural features of MBP. The modular design of our scaffold allows the adaptation of new DARPins through minor amino-acid-sequence modifications, enabling the binding and visualization of a diverse array of proteins. The high symmetry and near-spherical shape of the scaffold not only mitigates the prevalent challenge of preferred particle orientation in cryo-EM but also significantly reduces the demands of image collection and data processing. This approach presents a versatile solution, breaking through the size constraints that have traditionally limited single-particle cryo-EM.

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Primary Citation of related structures