9Q1B | pdb_00009q1b

MS2 bacteriophage coat protein after reassembly as a nanocrate (MS2nc) with no cargo and with waters modeled

• PDB DOI: https://doi.org/10.2210/pdb9Q1B/pdb
• EM Map EMD-72122: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Escherichia phage MS2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-08-13 Released: 2025-08-27 
• Deposition Author(s): Zimanyi, C.M., Bobe, D., Jenkins, M.C., Kopylov, M.
• Funding Organization(s): Simons Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 1.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Overcoming air-water interface-induced artifacts in cryo-EM with protein nanocrates.

Jenkins, M.C., Bobe, D., Johnston, J.D., Cheung, J., Karasawa, A., Zimanyi, C.M., Dermanci, O., McManus, C.T., Finn, M.G., de Marco, A., Kopylov, M.

(2026) Nat Methods 23: 1798-1804

• PubMed: 42637978 
• DOI: https://doi.org/10.1038/s41592-026-03184-w
• Primary Citation Related Structures: 
  9Q1B, 9Q1D


• PubMed Abstract: 
  

  Contact with the air-water interface can bias the orientation of macromolecules during cryo-electron microscopy sample preparation, leading to uneven sample distribution, preferred orientation and damage to the molecules of interest. To prevent this, we describe a method to encapsulate target proteins within highly hydrophilic, structurally homogeneous and stable protein shells, which we refer to as 'nanocrates' for this purpose. Here we describe the packaging, data acquisition and reconstruction of three proof-of-principle examples, each illuminating a different aspect of the method: apoferritin (demonstrating high-resolution), thyroglobulin (solving a known preferred orientation problem) and 7,8-dihydroneopterin aldolase (a structure previously uncharacterized by cryo-electron microscopy).

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Organizational Affiliation: 
• School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.
School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA. [e-mail].
Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA. [e-mail].
Department of Biochemistry and Biophysics, Columbia University, New York, NY, USA. [e-mail].
Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA. [e-mail].
CZI Biohub, Redwood City Site, Redwood City, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 41.22 kDa 
• Atom Count: 3,123 
• Modeled Residue Count: 387 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	129	Escherichia phage MS2	Mutation(s): 0
UniProt
Find proteins for P03612 (Escherichia phage MS2) Explore P03612  Go to UniProtKB:  P03612

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 1.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Zimanyi, C.M., Bobe, D., Jenkins, M.C., Kopylov, M.

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Funding Organization	Location	Grant Number
Simons Foundation	United States	SF349247
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI148382
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA247484

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2026-03-11
  Changes: Data collection, Database references
• Version 1.2: 2026-09-09
  Changes: Data collection, Database references
• Version 1.3: 2026-09-16
  Changes: Data collection, Database references