7XCA | pdb_00007xca

Crystal structure of the porcine astrovirus capsid spike domain

• PDB DOI: https://doi.org/10.2210/pdb7XCA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Mamastrovirus 3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-23 Released: 2023-03-29 
• Deposition Author(s): Pan, L.X., Zhang, W.C., Yang, D.F., Yang, L.Y., Liu, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure analysis of porcine astrovirus capsid spike and spike/neutralizing antibody complexes.

Pan, L.X., Zhang, W.C., Yang, D.F., Yang, L.Y., Liu, H.

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: gel filtration

Macromolecule Content

• Total Structure Weight: 59.57 kDa 
• Atom Count: 3,314 
• Modelled Residue Count: 420 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein spike domain	A, B	271	Mamastrovirus 3	Mutation(s): 0
UniProt
Find proteins for W5X1V8 (Porcine astrovirus 1) Explore W5X1V8  Go to UniProtKB:  W5X1V8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.48	α = 90
b = 105.17	β = 111.91
c = 47.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Pan, L.X., Zhang, W.C., Yang, D.F., Yang, L.Y., Liu, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31860245
National Natural Science Foundation of China (NSFC)	China	31960203
National Natural Science Foundation of China (NSFC)	China	31760735

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection, Refinement description