6C6Q

Crystal Structure of the Murine Norovirus VP1 P Domain in complex with the CD300lf Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor.

Nelson, C.A.Wilen, C.B.Dai, Y.N.Orchard, R.C.Kim, A.S.Stegeman, R.A.Hsieh, L.L.Smith, T.J.Virgin, H.W.Fremont, D.H.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E9201-E9210


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A, B
303Murine norovirus 1Mutation(s): 0 
Find proteins for Q80J94 (Murine norovirus 1)
Go to UniProtKB:  Q80J94
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CMRF35-like molecule 1
D, F
113Mus musculusMutation(s): 0 
Gene Names: Cd300lf (Clm1, Lmir3)
Find proteins for Q6SJQ7 (Mus musculus)
Go to UniProtKB:  Q6SJQ7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, D, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.712α = 90.00
b = 135.245β = 90.00
c = 139.516γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI109725
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI127552

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Database references