8A2G | pdb_00008a2g

Crystal structure of Sebokelevirus 2A2 protein

• PDB DOI: https://doi.org/10.2210/pdb8A2G/pdb

• Classification: VIRAL PROTEIN
• Organism(s): parechovirus C1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-03 Released: 2023-06-14 
• Deposition Author(s): Zhu, L., Von Castelmur, E., Whang, X., Ren, J., Fry, E., Perrakis, A., Stuart, D.I.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Structural plasticity of 2A proteins in the Parechovirus family

Von Castelmur, E., Zhu, L., Perrakis, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 32.05 kDa 
• Atom Count: 2,565 
• Modeled Residue Count: 290 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2A2 protein	A, B	146	parechovirus C1	Mutation(s): 0
UniProt
Find proteins for S0DHJ0 (parechovirus C1) Explore S0DHJ0  Go to UniProtKB:  S0DHJ0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.202 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.35	α = 90
b = 69.73	β = 90
c = 57.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Zhu, L., Von Castelmur, E., Whang, X., Ren, J., Fry, E., Perrakis, A., Stuart, D.I.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description