8EU5 | pdb_00008eu5

Acheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure

• PDB DOI: https://doi.org/10.2210/pdb8EU5/pdb
• EM Map EMD-28604: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Solenopsis invicta-associated densovirus
• Expression System: Acheta domesticus
• Mutation(s): No 


• Deposited: 2022-10-18 Released: 2022-11-09 
• Deposition Author(s): Penzes, J.J., McKenna, R., Tijssen, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome

Penzes, J.J., Pham, H.T., Chipman, P., Smith, E., McKenna, R., Tijssen, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 36.29 kDa 
• Atom Count: 2,551 
• Modeled Residue Count: 318 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	318	Solenopsis invicta-associated densovirus	Mutation(s): 0  Gene Names: CP
UniProt
Find proteins for A0A891H5C3 (Solenopsis invicta-associated densovirus) Explore A0A891H5C3  Go to UniProtKB:  A0A891H5C3

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.8.9.3
MODEL REFINEMENT	PHENIX	1.10.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Penzes, J.J., McKenna, R., Tijssen, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082946
National Institutes of Health/Office of the Director	United States	OD018142
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	RR025080

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Source and taxonomy
• Version 1.2: 2024-06-19
  Changes: Data collection, Derived calculations