3D Structures Reconstruction Service

In modern structural biology, resolving the 3D structures of proteins, nucleic acids, and their complexes is fundamental to understanding molecular mechanisms, identifying novel drug targets, and designing biologics. Compared to traditional techniques such as X-ray crystallography and NMR spectroscopy, Cryo-electron microscopy (Cryo-EM), particularly when combined with single particle analysis (SPA), provides powerful capabilities for high-resolution structure determination of non-crystalline, flexible, and complex biomolecules.

 

MtoZ Biolabs leverages a state-of-the-art Cryo-EM platform, advanced reconstruction algorithms and an experienced structural biology team to offer high-quality, customizable 3D Structures Reconstruction Service that supports comprehensive structural investigations for academic and pharmaceutical research.

 

Services at MtoZ Biolabs

Our 3D Structures Reconstruction Service focuses on the modeling of diverse biological targets. Using Cryo-EM and cutting-edge reconstruction software, we provide accurate and reproducible 3D structural models for:

·  Antibody–Antigen Complexes

Includes structures of neutralizing antibodies bound to their epitopes, supporting vaccine development and antibody engineering.

·  G Protein-Coupled Receptors (GPCRs)

Captures conformational states relevant to signaling and ligand binding.

·  Ion Channels & Solute Carrier (SLC) Transporters

Covers calcium, sodium, and potassium channels; elucidates ion selectivity and transport mechanisms.

·  Multimeric Complexes & Soluble Proteins

Resolves structures of large assemblies, signaling complexes, and metabolic enzymes.

·  Membrane Proteins & Transmembrane Receptors

Includes RTKs, integrins, and transporters; applicable to both monomeric and oligomeric forms.

·  Protein–Nucleic Acid Complexes

Supports studies on DNA/RNA binding, transcription regulation, and RNA splicing.

·  RNA Molecules

Covers miRNA, siRNA, and lncRNA structures, either in isolation or in complex with proteins.

 

Analysis Workflow

MtoZ Biolabs offers an end-to-end workflow for Cryo-EM-based 3D structure determination:

1. Sample Preparation & Vitrification

Samples are embedded in amorphous ice by plunge freezing to preserve native conformations.

 

2. Image Acquisition

High-resolution micrographs are collected using top-tier Cryo-EM instruments (e.g., Titan Krios) under low-dose conditions.

 

3. Image Preprocessing & Particle Picking

Automated pipelines perform motion correction, artifact removal, and high-quality particle selection.

 

4. 2D Classification & Initial Model Generation

Class averages are computed to enhance signal-to-noise and construct preliminary 3D density maps.

 

5. 3D Reconstruction & Refinement

Final models are refined using tools such as cryoSPARC and RELION to improve resolution and accuracy.

 

6. Validation & Functional Annotation

Global and local resolution are assessed; conformational heterogeneity is analyzed; biological interpretation is supported.

 

Service Advantages

✔ Advanced Analysis Platform: Equipped with high-end Cryo-EM microscopes, energy filters, and automated acquisition systems.

✔ Robust Algorithm Integration: Supports RELION, cryoSPARC, and cisTEM to handle heterogeneous or flexible particles.

✔ High Data Quality: Optimized vitrification and image preprocessing improve contrast and resolution.

✔ Customizable Projects: Tailored data acquisition and modeling strategies based on research goals.

✔ Expert Team Support: Multidisciplinary scientists provide full-cycle support from raw data to publication-ready models.

✔ Cross-platform Modeling: Enables integration with X-ray, AlphaFold, and hybrid modeling strategies.

 

Case Study

Case 1

In a 2024 study, researchers employed neural field-based 3D reconstruction to overcome resolution and anisotropy limitations of Fourier-based methods. The model mapped spatial coordinates to density values, improving structural precision on multiple homogeneous and heterogeneous datasets, including SARS-CoV-2.

 



Huang, Y. et al. Nat. Mach. Intell. 2024

 

This research demonstrates the potential of deep learning to enhance structural resolution. MtoZ Biolabs integrates such advances into our 3D Structures Reconstruction Service to support complex macromolecule analysis, from protein assemblies to drug targets.

 

FAQ

Q1: Can I request specific steps instead of the full service?

Yes, we offer modular services such as 2D classification, initial model generation, or 3D refinement based on your project phase.

 

Q2: How do I know if my sample is suitable for Cryo-EM reconstruction?

Suitability depends on molecular weight (>100 kDa preferred), homogeneity, conformational stability, and distribution in ice. We offer negative-stain screening and 2D class evaluation for pre-assessment.

 

Q3: What resolution levels can be achieved?

We support reconstructions from ~10 Å to near-atomic resolution (<3 Å), depending on sample quality and processing conditions.

 

High-resolution 3D structures serve as the foundation for mechanistic understanding and precision drug design. MtoZ Biolabs’ 3D Structures Reconstruction Service delivers reliable, publication-grade results with flexibility for diverse structural biology needs.


Contact us to discuss your project and receive customized recommendations.