6JJC | pdb_00006jjc

Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP

• PDB DOI: https://doi.org/10.2210/pdb6JJC/pdb
• EM Map EMD-9706: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Macrobrachium rosenbergii nodavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-25 Released: 2019-05-01 
• Deposition Author(s): Chang, W.H., Wang, C.H., Lin, H.H., Lin, S.Y., Chong, S.C., Wu, Y.Y.
• Funding Organization(s): Ministry of Science and Technology (Taiwan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP

Chang, W.H., Wang, C.H., Lin, H.H., Lin, S.Y., Chong, S.C., Wu, Y.Y.

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)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 124.72 kDa 
• Atom Count: 4,753 
• Modeled Residue Count: 602 
• Deposited Residue Count: 1,113 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	371	Macrobrachium rosenbergii nodavirus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	3374

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-01 
Deposition Author(s): Chang, W.H., Wang, C.H., Lin, H.H., Lin, S.Y., Chong, S.C., Wu, Y.Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 103-2321-B-001-048
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 104-2321-B-001-019
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 105-2321-B-001-009
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 106-0210-01-15-02
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 106-0210-01-15-04
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 107-0210-01-19-01
Ministry of Science and Technology (Taiwan)	Taiwan	MOST 107-0210-01-19-02

Revision History  

• Version 1.0: 2019-05-01
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Derived calculations