8AY4 | pdb_00008ay4

Human rhinovirus 2 virion in situ

• PDB DOI: https://doi.org/10.2210/pdb8AY4/pdb
• EM Map EMD-15710: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): rhinovirus A2
• Mutation(s): No 


• Deposited: 2022-09-01 Released: 2023-09-13 
• Deposition Author(s): Ishemgulova, A., Mukhamedova, L., Trebichalska, Z., Payne, P., Smerdova, L., Moravcova, J., Hrebik, D., Buchta, D., Skubnik, K., Fuzik, T., Novacek, J., Plevka, P.
• Funding Organization(s): Czech Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Endosome rupture enables enteroviruses to infect cells.

Ishemgulova, A.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 240-mer - A60B60C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 240-mer - A120B60C60 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 87.46 kDa 
• Atom Count: 6,143 
• Modeled Residue Count: 781 
• Deposited Residue Count: 781 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A	269	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP2	B	250	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	C	237	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP4	D	25	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	ISOLDE	1.4

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Ishemgulova, A., Mukhamedova, L., Trebichalska, Z., Payne, P., Smerdova, L., Moravcova, J., Hrebik, D., Buchta, D., Skubnik, K., Fuzik, T., Novacek, J., Plevka, P.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	GX19-25982X

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release