8A5T

Capsid structure of the L-A helper virus from native viral communities

• PDB DOI: https://doi.org/10.2210/pdb8A5T/pdb
• EM Map EMD-15189: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2022-06-16 Released: 2023-12-20 
• Deposition Author(s): Schmidt, L., Tueting, C., Stubbs, M.T., Kastritis, P.L.
• Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG), European Regional Development Fund

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts

Schmidt, L., Tuting, C., Kyrilis, F.L., Hamdi, F., Semchonok, D.A., Hause, G., Meister, A., Ihling, C., Shah, P.N.M., Stubbs, M.T., Sinz, A., Stuart, D.I., Kastritis, P.L.

(2022) Biorxiv 

• DOI: https://doi.org/10.1101/2022.07.15.498668

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 120-mer - A120 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 152.14 kDa 
• Atom Count: 10,302 
• Modelled Residue Count: 1,302 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B	680	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32503 (Saccharomyces cerevisiae virus L-A) Explore P32503  Go to UniProtKB:  P32503

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.6
MODEL REFINEMENT	PHENIX	dev-4379
RECONSTRUCTION	cryoSPARC	v3.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Schmidt, L., Tueting, C., Stubbs, M.T., Kastritis, P.L.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	03Z22HN23
German Federal Ministry for Education and Research	Germany	03Z22HI2
German Federal Ministry for Education and Research	Germany	03COV04
German Research Foundation (DFG)	Germany	391498659
European Regional Development Fund	European Union	EFRE: ZS/2016/04/78115

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release