Cryo-EM De Novo Structure Analysis Service

Cryo-electron microscopy (Cryo-EM) de novo structure analysis is a powerful strategy for resolving high-resolution structures of proteins with no known reference models. The term de novo indicates that the target protein and its homologs are absent from the Protein Data Bank (PDB), making the structure determination both innovative and technically demanding. This approach is particularly suited for novel targets, membrane proteins, and multicomponent complexes.

 

Unlike conventional crystallography, Cryo-EM does not require crystallization and offers superior advantages such as minimal sample requirements, native-state imaging, and atomic-level precision. At MtoZ Biolabs, we offer a fully integrated Cryo-EM De Novo Structure Analysis Service—covering everything from sample evaluation to atomic model generation—to help researchers overcome the challenges of structural biology and drug discovery.

 

Services at MtoZ Biolabs

MtoZ Biolabs provides a comprehensive Cryo-EM De Novo Structure Analysis Service that supports a wide range of proteins and macromolecular complexes including:

• Antibody–antigen complexes
• G protein-coupled receptors (GPCRs)
• Ion channels and multimeric transporters
• Multiprotein assemblies
• Soluble and membrane proteins (≥100 kDa)
• Protein–nucleic acid complexes, solute carriers (SLCs), viral particles, and more

 



Si, D. et al. WIRES COMPUT MOL SCI. 2021.

Figure 1. Schematic Diagram of Cryo-EM De Novo Modeling Workflow

 

Simply provide your sample, and MtoZ Biolabs will deliver a comprehensive, end-to-end solution—from sample evaluation, vitrification, and data collection to image processing, 3D reconstruction, and atomic model building—ensuring high-quality structural insights with minimal effort on your part.

 

Why Choose MtoZ Biolabs?

MtoZ Biolabs' Cryo-EM De Novo Structure Analysis Service delivers reliable support for high-resolution structural determination of novel biomolecules:

✅  No template required: Ideal for novel proteins lacking homologous models

✅  Minimal sample input: Requires as little as 100 μL at 2 mg/mL concentration

✅  Conformational diversity handling: 2D/3D classification reveals multiple states

✅  High-throughput data analysis: Supports automatic processing of millions of particles

✅  Broad applicability: Suitable for peptides, membrane proteins, and large complexes

✅  One-time-charge: Our pricing is transparent, no hidden fees or additional costs.

 

Applications

Our Cryo-EM De Novo Structure Analysis Service is widely applicable across academic and industrial settings for:

·  New protein structure determination: Elucidating first-in-class biological targets

·  Lead optimization: Visualizing protein–ligand interfaces to support structure-guided design

·  Mechanistic studies: Understanding function through conformational transitions

·  Multistate modeling: Resolving dynamic molecular architectures

·  Vaccine and antibody development: Analyzing viral epitopes and antibody binding

 

Case Study

Case 1: De Novo Modeling of Nucleic Acids from Cryo-EM Maps

A 2024 study introduced a deep learning–based de novo tool, EM2NA, for reconstructing DNA/RNA structures from cryo-EM density maps. Capable of resolving structures at 2.0–5.0 Å resolution, EM2NA achieved 83.15% residue coverage with an average backbone RMSD of 1.06 Å—outperforming existing tools such as CryoREAD and ModelAngelo. This method successfully modeled nucleic acid fragments ranging from 10 to 5347 nt across 263 unannotated cryo-EM datasets, demonstrating excellent scalability in template-free modeling.

 



 Li, T. et al. Nat. Commun. 2024.

 

MtoZ Biolabs integrates high-resolution cryo-EM imaging with AI-assisted structure modeling to deliver precise structural analysis of proteins, DNA, and RNA. This service supports applications in nucleic acid drug design, structural biology, and synthetic biology.

 

FAQ

Q1: How does the service address conformational heterogeneity?

Our multi-stage 2D and 3D classification workflows effectively resolve structural polymorphisms within heterogeneous samples. Distinct conformational states are reconstructed independently without compromising resolution—ideal for capturing dynamic intermediates, catalytic states, or flexible assemblies.

 

Q2: What advantages does Cryo-EM offer for membrane proteins?

Membrane proteins are often difficult to crystallize due to their hydrophobic nature. MtoZ Biolabs employs graphene oxide support films, optimized buffers, and orientation bias control to stabilize particles, improving imaging quality and reconstruction resolution for complex transmembrane systems.

 

Q3: How is atomic modeling achieved without a homologous template?

When template-based modeling is not feasible, our team combines high-resolution Cryo-EM density maps with AI-based de novo prediction tools to build accurate atomic models, enabling reliable identification of functional domains and binding interfaces.

 

If you're exploring de novo structure determination of novel proteins or complexes, MtoZ Biolabs is your trusted partner. With a robust imaging platform, expert team, and end-to-end pipeline, our Cryo-EM De Novo Structure Analysis Service empowers cutting-edge structural research and biopharmaceutical innovation. Contact us for customized support.