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., Finn, M.G., de Marco, A., Kopylov, M.

To be published.

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