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- PDB-6c74: Crystal Structure of Murine CD300lf in complex with phosphocholine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6c74 | |||||||||
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Title | Crystal Structure of Murine CD300lf in complex with phosphocholine | |||||||||
![]() | CMRF35-like molecule-1 | |||||||||
![]() | LIPID BINDING PROTEIN / CD300lf / IgV-like domain / myeloid receptor / CMRF-35-like molecule-1 / CLM-1 / CLM1 / DIR2 / IREM1 / LMIR3 / PIGR3. IgSF13 | |||||||||
Function / homology | ![]() interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding ...interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / negative regulation of apoptotic cell clearance / interleukin-4 receptor binding / positive regulation of interleukin-4-mediated signaling pathway / negative regulation of mast cell activation / ceramide binding / positive regulation of apoptotic cell clearance / TRIF-dependent toll-like receptor signaling pathway / phosphatidylserine binding / osteoclast differentiation / transmembrane signaling receptor activity / virus receptor activity / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Nelson, C.A. / Fremont, D.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor. Authors: Christopher A Nelson / Craig B Wilen / Ya-Nan Dai / Robert C Orchard / Arthur S Kim / Roderick A Stegeman / Leon L Hsieh / Thomas J Smith / Herbert W Virgin / Daved H Fremont / ![]() Abstract: Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric ...Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its cellular receptor CD300lf. CD300lf binds the P domain with a 2:2 stoichiometry, engaging a cleft between the AB and DE loops of the P2 subdomain at a site that overlaps the epitopes of neutralizing antibodies. We also identify that bile acids are cofactors enhancing MNoV cell-binding and infectivity. Structures of CD300lf-P domain in complex with glycochenodeoxycholic acid (GCDCA) and lithocholic acid (LCA) reveal two bile acid binding sites at the P domain dimer interface distant from receptor binding sites. The structural determinants for receptor and bile acid binding are supported by numerous biophysical assays utilizing interface residue mutations. We find that the monomeric affinity of CD300lf for the P domain is low and is divalent cation dependent. We have also determined the crystal structure of CD300lf in complex with phosphocholine, revealing that MNoV engages its receptor in a manner mimicking host ligands including similar metal coordination. Docking of the cocomplex structures onto a cryo-EM-derived model of MNoV suggests that each virion can make multiple CD300lf engagements, and thus, infection may be driven by the avidity of cell surface clustered CD300lf. These studies identify multiple potential modulators of norovirus infection that may act to regulate the interaction between the viral capsid P domain and its cognate cellular receptor. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61 KB | Display | ![]() |
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PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431 KB | Display | ![]() |
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Full document | ![]() | 431 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7564C ![]() 6c6qC ![]() 6crjC ![]() 6e47C ![]() 6e48C ![]() 5fflS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12554.189 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 20-130) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PC / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 0.1 M Phosphocholine, pH 7.4, 33% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CMOS / Date: Oct 29, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.35→40.02 Å / Num. obs: 35969 / % possible obs: 98.4 % / Redundancy: 11.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.039 / Rrim(I) all: 0.138 / Net I/σ(I): 10.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5FFL Resolution: 1.358→34.552 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.13 Å2 / Biso mean: 17.7317 Å2 / Biso min: 7.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.358→34.552 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26
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