Protein Degraders and Ternary Complexes Structure Characterization Service | Cryo-EM

In recent years, targeted protein degradation (TPD) has emerged as a transformative approach in drug development. By inducing the selective degradation of disease-associated proteins, this strategy effectively modulates key biological pathways, particularly demonstrating great potential in cancer therapy. Protein degraders, such as PROTACs (Proteolysis Targeting Chimeras), function by forming ternary complexes that include the target protein, the degrader molecule, and an E3 ubiquitin ligase. This assembly facilitates the ubiquitination and subsequent degradation of the target protein. Therefore, a clear structural understanding of how degraders engage both the target protein and the E3 ligase is essential for mechanism elucidation, activity optimization, and rational drug design.

 



Békés, M. et al. Nat Rev Drug Discov. 2022.

Figure 1. The Mechanism of PROTAC-Mediated Targeted Protein Degradation

 

MtoZ Biolabs offers high-quality, high-resolution Protein Degraders and Ternary Complexes Structure Characterization Service based on Cryo-EM. Our services support researchers in gaining deep mechanistic insights and accelerating drug discovery efforts.

 

Technical Principles

Cryo-electron microscopy (Cryo-EM) is an advanced structural biology technique that allows the visualization of macromolecular complexes without requiring crystallization. It is particularly suited for studying structurally complex and conformationally heterogeneous ternary complexes that are difficult to resolve using traditional X-ray crystallography.

 

By rapidly vitrifying samples under near-native conditions, Cryo-EM preserves the natural conformation of proteins and complexes. The vitrified samples are then imaged using an electron beam to generate 2D projections, which are computationally reconstructed into high-resolution 3D models. This enables the detailed visualization of spatial relationships among the degrader, target protein, and E3 ligase.

 

Analysis Workflow

MtoZ Biolabs’ Protein Degraders and Ternary Complexes Structure Characterization Service based on Cryo-EM includes the following standardized steps:

1. Sample Preparation and Quality Control

Submitted ternary complex samples are subjected to rigorous QC to ensure concentration, purity, and stability meet imaging requirements.

 

2. Grid Preparation and Vitrification

Advanced vitrification techniques are used to quickly freeze the sample on grids in liquid ethane, maintaining its native structure.

 

3. Data Collection and Image Processing

High-resolution micrographs are acquired using state-of-the-art cryo-electron microscopes, followed by particle selection and 3D reconstruction using dedicated software.

 

4. 3D Reconstruction and Model Refinement

The resulting density maps are refined and used to build accurate structural models, revealing atomic-level interactions.

 

5. Structural Interpretation and Reporting

A detailed report is provided, covering binding modes, interaction interfaces, conformational changes, and potential mechanistic insights.

 

Service Advantagess

1. High-Resolution Structural Analysis: Advanced Cryo-EM systems enable atomic or near-atomic resolution, ideal for visualizing key interactions.

 

2. No Need for Crystallization: Suitable for flexible, dynamic, and heterogeneous complexes that cannot be crystallized.

 

3. Experienced Analysis Team: Our team combines expertise in structural biology and drug development for accurate interpretation.

 

4. End-to-End Workflow: Full support from sample preparation to data interpretation ensures reliable and efficient service delivery.

 

Applications

This Protein Degraders and Ternary Complexes Structure Characterization Service based on Cryo-EM is widely applicable across both drug discovery and basic research, including but not limited to:

 

1. Optimization of Protein Degraders: Identifying interaction sites and binding modes to guide rational compound modification.

 

2. Mechanism of Action Studies: Understanding the formation and function of ternary complexes to reveal degradation mechanisms.

 

3. Target Validation and Screening: Structurally confirming molecular interactions to support compound screening and validation.

 

4. Fundamental Structural Biology: Gaining structural insights into protein complexes for functional and mechanistic studies.

 

Case Study

1. Protein Ternary Complexes Structure Characterization Based on Cryo-EM

This study uncovers the mechanism of a novel class of targeted protein degraders known as intramolecular bivalent glues (IBGs). Unlike traditional PROTACs that bridge the target protein and E3 ligase in trans, IBGs simultaneously bind two adjacent domains of the target protein (such as BRD4) in cis, inducing a conformational change that promotes interaction with E3 ligases like DCAF11 or DCAF16. This conformational “gluing” enhances surface complementarity, enabling efficient ubiquitination and degradation. Structural analysis of the BRD4–IBG1–DCAF16 ternary complex revealed critical binding interfaces and guided the design of improved degraders with picomolar potency. Protein Degraders and Ternary Complexes Structure Characterization Service enables structural analysis of ternary complexes formed by multi-domain proteins, degraders, and E3 ligases, especially those involving conformational regulation in cis. It supports the investigation of non-classical degradation mechanisms and facilitates structure-based optimization of novel degrader molecules.

 



Hsia, O. et al. Nature. 2024.

Figure 2. The Structure of the Ternary Complex by Cryo-EM 

 

2. Mechanistic Insights Into a Heterobifunctional Degrader-Induced PTPN2/N1 Complex

This study reports the development and structural characterization of potent heterobifunctional degraders (Cmpd-1 and Cmpd-2) targeting phosphatases PTPN2 and PTPN1, which are key immuno-oncology targets. These degraders promote ternary complex formation between PTPN2/N1 and the CRL4^CRBN E3 ligase, leading to effective degradation in cells and animal models. Crystallography revealed the degrader–PTPN2 interaction interface, while high-resolution cryo-EM elucidated the structure of the DDB1–CRBN/Cmpd-1/PTPN2 complex. Despite its conformational heterogeneity, the ternary complex demonstrates degrader-induced proximity between CRBN and PTPN2. Molecular dynamics simulations further revealed dynamic motions and interaction surfaces within the complex, highlighting the flexible nature of degrader-induced ternary assemblies. Protein Degraders and Ternary Complexes Structure Characterization Service enables structural resolution of dynamic and conformationally heterogeneous ternary complexes formed by degraders, targets, and E3 ligases. It supports integrated workflows combining cryo-EM and computational modeling to capture flexible protein assemblies and degrader-mediated proximity effects.

 



Hao, Q. et al. Commun Chem. 2024.

 Figure 3. Cryo-EM Map Density of the Degrader-Induced PTPN2/N1 Complex

 

FAQ

Q1: What types of samples are suitable for Cryo-EM structural analysis?

A1: Cryo-EM is ideal for complexes that are difficult to crystallize, including flexible and conformationally heterogeneous samples like ternary degrader complexes.

 

Q2: What are the basic sample requirements?

A2: We typically recommend samples with >90% purity and concentrations above \~1 mg/mL. Specific requirements may vary depending on the project.

 

Q3: What is the expected turnaround time?

A3: The typical service timeline is 4–8 weeks, depending on sample complexity and project scope.

 

Q4: What deliverables are included in the final report?

A4: Deliverables include high-quality density maps, refined structural models (PDB format), and a comprehensive interpretation report.

 

Q5: How does Cryo-EM compare to X-ray crystallography?

A5: Cryo-EM does not require crystallization and captures proteins in near-native states, making it especially useful for heterogeneous or flexible complexes.

 

As protein degraders gain traction in precision medicine and next-generation drug discovery, structural analysis is becoming a critical factor in guiding their development. MtoZ Biolabs is committed to providing reliable Protein Degraders and Ternary Complexes Structure Characterization Service using our advanced Cryo-EM platform. Whether you're optimizing a lead compound or validating a new molecular mechanism, our rigorous workflows and scientific expertise ensure high-quality insights. Contact us today for project evaluation and customized service solutions.