9QVE | pdb_00009qve

Satellite Tobacco Necrosis Virus-1

• PDB DOI: https://doi.org/10.2210/pdb9QVE/pdb
• EM Map EMD-53395: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Satellite tobacco necrosis virus 1
• Expression System: Nicotiana benthamiana
• Mutation(s): No 


• Deposited: 2025-04-11 Released: 2025-05-07 
• Deposition Author(s): Saunders, K., Shah, S., Peyret, H., Meshcheriakova, Y., Richardson, J., Eltschkner, S., Lawson, D.M., Lomonossoff, G.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

The specificity of RNA packaging in isometric RNA plant viruses is principally determined by replication

Saunders, K., Shah, S., Peyret, H., Meshcheriakova, Y., Richardson, J., Eltschkner, S., Lawson, D.M., Lomonossoff, G.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by UCSF CHIMERA 1.17.3_b42480. (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 21.81 kDa 
• Atom Count: 1,430 
• Modeled Residue Count: 184 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	196	Satellite tobacco necrosis virus 1	Mutation(s): 0
UniProt
Find proteins for P03606 (Satellite tobacco necrosis virus 1) Explore P03606  Go to UniProtKB:  P03606

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.77 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.21.2_5419:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-07 
Deposition Author(s): Saunders, K., Shah, S., Peyret, H., Meshcheriakova, Y., Richardson, J., Eltschkner, S., Lawson, D.M., Lomonossoff, G.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X01097X/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/Y005732/1

Revision History  

• Version 1.0: 2025-05-07
  Type: Initial release