3CZ3 | pdb_00003cz3

Crystal structure of Tomato Aspermy Virus 2b in complex with siRNA

• PDB DOI: https://doi.org/10.2210/pdb3CZ3/pdb
• NAKB: 3CZ3

• Classification: VIRAL PROTEIN/RNA
• Organism(s): Tomato aspermy virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-27 Released: 2009-05-05 
• Deposition Author(s): Ma, J.B., Li, F., Ding, S.W., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 
  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

Structural Basis for siRNA Recognition by 2b, a Viral Suppressor of Non-Cell Autonomous RNA Silencing

Ma, J.B., Li, F., Ding, S.W., Patel, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 57.49 kDa 
• Atom Count: 5,166 
• Modeled Residue Count: 298 
• Deposited Residue Count: 356 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein 2b	E [auth A], F [auth B], G [auth C], H [auth D]	70	Tomato aspermy virus	Mutation(s): 0  Gene Names: RNA2
UniProt
Find proteins for Q8UYT3 (Tomato aspermy virus) Explore Q8UYT3  Go to UniProtKB:  Q8UYT3

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*GP*UP*AP*CP*GP*CP*GP*GP*AP*AP*UP*AP*CP*UP*UP*CP*GP*A)-3')	A [auth E], C [auth G]	19	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*CP*GP*AP*AP*GP*UP*AP*UP*UP*CP*CP*GP*CP*GP*UP*AP*CP*G)-3')	B [auth F], D [auth H]	19	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free:  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.9	α = 90
b = 165.67	β = 90
c = 35.59	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Ma, J.B., Li, F., Ding, S.W., Patel, D.J.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references