7ER1

Crystal structure of capsid P domain of norovirus GI.3 VA115 complexed with Gala1-3Galb1-4Glc

• PDB DOI: https://doi.org/10.2210/pdb7ER1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus GI.3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-05-05 Released: 2022-05-11 
• Deposition Author(s): Chen, Y.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.220 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 141.52 kDa 
• Atom Count: 9,973 
• Modelled Residue Count: 1,206 
• Deposited Residue Count: 1,308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid P domain	A, B, C, D	327	Norovirus GI.3	Mutation(s): 0
UniProt
Find proteins for I3V9L6 (Norovirus Hu/GI.3/1999) Explore I3V9L6  Go to UniProtKB:  I3V9L6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose	E	2		N/A
Glycosylation Resources
GlyTouCan:  G24432YB GlyCosmos:  G24432YB GlyGen:  G24432YB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.220 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.29	α = 102.28
b = 59.637	β = 96.72
c = 91.419	γ = 109.77

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-11 
Deposition Author(s): Chen, Y.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2017YFC0840300

Revision History  

• Version 1.0: 2022-05-11
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Database references
• Version 1.2: 2022-08-03
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description