5KOV

Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-A resolution

• PDB DOI: https://doi.org/10.2210/pdb5KOV/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human astrovirus 2, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2016-07-01 Released: 2016-11-09 
• Deposition Author(s): Bogdanoff, W.A., DuBois, R.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.288 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 422.56 kDa 
• Atom Count: 25,943 
• Modelled Residue Count: 3,263 
• Deposited Residue Count: 3,832 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid polyprotein VP90	A, D [auth B], E [auth H], H [auth G], I [auth N], L [auth M], M [auth S], P [auth T]	228	Human astrovirus 2	Mutation(s): 0  Gene Names: ORF2
UniProt
Find proteins for Q82446 (Human astrovirus-2) Explore Q82446  Go to UniProtKB:  Q82446

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PL-2 scFv chain	B [auth C], C [auth E], F [auth K], G [auth I], J [auth Q], K [auth O], N [auth W], O [auth U]	251	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	Q [auth C], R [auth E], S [auth K], T [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.288 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.998	α = 90
b = 199.998	β = 90
c = 157.515	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Bogdanoff, W.A., DuBois, R.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI095369

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2016-11-16
  Changes: Database references
• Version 1.2: 2017-01-18
  Changes: Database references
• Version 1.3: 2017-09-06
  Changes: Author supporting evidence
• Version 1.4: 2017-11-01
  Changes: Author supporting evidence
• Version 1.5: 2019-12-11
  Changes: Author supporting evidence
• Version 1.6: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.7: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary