9Y2Z | pdb_00009y2z

Icosahedral symmetric structure of an expansion intermediate of Turnip Crinkle Virus (Asymmetric Trimer Unit)

• PDB DOI: https://doi.org/10.2210/pdb9Y2Z/pdb
• EM Map EMD-72428: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Turnip crinkle virus
• Mutation(s): No 


• Deposited: 2025-09-01 Released: 2025-11-12 
• Deposition Author(s): Venkatakrishnan, V., Braet, S., Ramesh, R., Clawson, M.A., Laremore, T.N., Wong, S.M., Anand, G.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Asymmetric isopeptide bond steers directional genomic RNA egress from icosahedral virus.

Braet, S.M., Venkatakrishnan, V., Ramesh, R., Clawson, M.A., Laremore, T.N., Wong, S.M., Anand, G.S.

(2025) Sci Adv 11: eady4104-eady4104

• PubMed: 41385643 
• DOI: https://doi.org/10.1126/sciadv.ady4104
• Primary Citation of Related Structures:  
  9Y2Z, 9Y31


• PubMed Abstract: 
  

  Icosahedral RNA viruses rely upon essential asymmetries for directional genome egress into the host cell. How these asymmetric egress points are built into the quaternary assembly of the virion is unknown. Here, we capture the structure and dynamics of a partially expanded virus disassembly intermediate, poised to release its spring-loaded genomic RNA. The structure shows highly localized density of RNA underneath surface fivefold axes on one-half of the viral particle. This polarity in RNA distribution is associated with a unique interchain isopeptide bond (glutamic acid-lysine), which flanks conserved high-affinity RNA binding sites. This singular isopeptide bond at the asymmetric egress site confers an essential "loaded-die" feature that is critical for steering genomic RNA egress into the host cell for virus propagation.

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Organizational Affiliation: 
• Department of Chemistry, Penn State University, University Park, PA 16802, USA.
Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore.
Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA.
Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 114.51 kDa 
• Atom Count: 6,230 
• Modeled Residue Count: 842 
• Deposited Residue Count: 1,053 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	351	Turnip crinkle virus	Mutation(s): 0
UniProt
Find proteins for P06663 (Turnip crinkle virus) Explore P06663  Go to UniProtKB:  P06663

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Venkatakrishnan, V., Braet, S., Ramesh, R., Clawson, M.A., Laremore, T.N., Wong, S.M., Anand, G.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM158169-01

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Data collection, Database references