7DOD

Capsid structure of human sapovirus

• PDB DOI: https://doi.org/10.2210/pdb7DOD/pdb
• EM Map EMD-30793: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN
• Expression System: Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2020-12-14 Released: 2021-12-15 
• Deposition Author(s): Miyazaki, N., Murakami, K., Oka, T., Iwasaki, K., Katayama, K., Murata, K.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Atomic structure of human sapovirus capsid by single particle cryo-electron microscopy

Miyazaki, N., Murakami, K., Oka, T., Iwasaki, K., Katayama, K., Murata, K.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 182.26 kDa 
• Atom Count: 11,916 
• Modelled Residue Count: 1,573 
• Deposited Residue Count: 1,695 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calicivirin	A [auth C], B [auth A], C [auth B]	565	Sapovirus Hu/GI.6/Nichinan/FP05284/2005/JPN	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Miyazaki, N., Murakami, K., Oka, T., Iwasaki, K., Katayama, K., Murata, K.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	20fk0108121h0402
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	JP16H00786

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2024-06-05
  Changes: Data collection, Derived calculations