2ZAH | pdb_00002zah

X-ray structure of Melon necrotic spot virus

• PDB DOI: https://doi.org/10.2210/pdb2ZAH/pdb

• Classification: VIRUS
• Organism(s): Melon necrotic spot virus
• Mutation(s): No 


• Deposited: 2007-10-05 Released: 2008-10-07 
• Deposition Author(s): Wada, Y., Tsukihara, T., Omura, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.224 (Depositor), 0.486 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of Melon necrotic spot virus

Wada, Y., Tanaka, H., Yamashita, E., Kubo, C., Ichiki-Uehara, T., Nakazono-Nagaoka, E., Omura, T., Tsukihara, T.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 8-13

• PubMed: 18097092 
• DOI: https://doi.org/10.1107/S1744309107066481
• Primary Citation Related Structures: 
  2ZAH


• PubMed Abstract: 
  

  The structure of melon necrotic spot virus (MNSV) was determined at 2.8 A resolution. Although MNSV is classified into the genus Carmovirus of the family Tombusviridae, the three-dimensional structure of MNSV showed a higher degree of similarity to tomato bushy stunt virus (TBSV), which belongs to the genus Tombusvirus, than to carnation mottle virus (CMtV), turnip crinkle virus (TCV) or cowpea mottle virus (CPMtV) from the genus Carmovirus. Thus, the classification of the family Tombusviridae at the genus level conflicts with the patterns of similarity among coat-protein structures. MNSV is one of the viruses belonging to the genera Tombusvirus or Carmovirus that are naturally transmitted in the soil by zoospores of fungal vectors. The X-ray structure of MNSV provides us with a representative structure of viruses transmitted by fungi.

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Organizational Affiliation: 
• Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.

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: 107.51 kDa 
• Atom Count: 7,095 
• Modeled Residue Count: 923 
• Deposited Residue Count: 993 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A, B, C	331	Melon necrotic spot virus	Mutation(s): 0
UniProt
Find proteins for P19899 (Melon necrotic spot virus) Explore P19899  Go to UniProtKB:  P19899

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNX	E [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.224 (Depositor), 0.486 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 375.004	α = 90
b = 375.004	β = 90
c = 375.004	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Wada, Y., Tsukihara, T., Omura, T.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-01-30
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description