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- PDB-6c74: Crystal Structure of Murine CD300lf in complex with phosphocholine -

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Basic information

Entry
Database: PDB / ID: 6c74
TitleCrystal Structure of Murine CD300lf in complex with phosphocholine
ComponentsCMRF35-like molecule-1
KeywordsLIPID BINDING PROTEIN / CD300lf / IgV-like domain / myeloid receptor / CMRF-35-like molecule-1 / CLM-1 / CLM1 / DIR2 / IREM1 / LMIR3 / PIGR3. IgSF13
Function / homology
Function and homology information


interleukin-13-mediated signaling pathway / negative regulation of MyD88-dependent toll-like receptor signaling pathway / interleukin-4 receptor binding / negative regulation of apoptotic cell clearance / 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 / interleukin-4 receptor binding / negative regulation of apoptotic cell clearance / 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 / virus receptor activity / identical protein binding / plasma membrane
Similarity search - Function
SHP2-interacting transmembrane adaptor protein, SIT / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHOCHOLINE / CMRF35-like molecule 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.358 Å
AuthorsNelson, C.A. / Fremont, D.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109725 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127552 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
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
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMRF35-like molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7783
Polymers12,5541
Non-polymers2242
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-8 kcal/mol
Surface area6160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.640, 40.058, 68.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CMRF35-like molecule-1 / CLM-1 / CD300 antigen-like family member F / Leukocyte mono-Ig-like receptor 3 / Myeloid-associated ...CLM-1 / CD300 antigen-like family member F / Leukocyte mono-Ig-like receptor 3 / Myeloid-associated immunoglobulin-like receptor 5 / MAIR-V


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.) Mus musculus (house mouse) / Gene: Cd300lf, Clm1, Lmir3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SJQ7
#2: Chemical ChemComp-PC / PHOSPHOCHOLINE / Phosphocholine


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 30.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 0.1 M Phosphocholine, pH 7.4, 33% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00004 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: Oct 29, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.35-1.375.62.0868700.4210.9442.30286.6
7.27-40.0210.90.0661710.9840.0210.0799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5FFL

5ffl


Resolution: 1.358→34.552 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.1894 3577 9.94 %
Rwork0.1651 --
obs0.1675 35969 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.13 Å2 / Biso mean: 17.7317 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 1.358→34.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 25 151 1053
Biso mean--25.32 26.66 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01920
X-RAY DIFFRACTIONf_angle_d1.2741246
X-RAY DIFFRACTIONf_chiral_restr0.092133
X-RAY DIFFRACTIONf_plane_restr0.007159
X-RAY DIFFRACTIONf_dihedral_angle_d12.985356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.358-1.37590.332980.3594915101372
1.3759-1.39470.30431120.3727950106274
1.3947-1.41460.36321130.33341083119684
1.4146-1.43570.35181300.32051182131291
1.4357-1.45820.28611340.28431210134495
1.4582-1.48210.26091470.27421293144098
1.4821-1.50760.23971400.249812721412100
1.5076-1.53510.37431420.283712991441100
1.5351-1.56460.23951400.225613061446100
1.5646-1.59650.20981410.196212861427100
1.5965-1.63120.25881460.192413031449100
1.6312-1.66920.22341400.176912991439100
1.6692-1.71090.2281360.164313111447100
1.7109-1.75720.22381470.164612731420100
1.7572-1.80890.20581450.15512841429100
1.8089-1.86730.18271420.161313011443100
1.8673-1.9340.24421380.18671265140398
1.934-2.01140.1571390.1451277141699
2.0114-2.1030.1381490.136812801429100
2.103-2.21380.16441420.129312891431100
2.2138-2.35250.18211400.16121277141798
2.3525-2.53410.14551430.140412821425100
2.5341-2.7890.15271450.140512821427100
2.789-3.19230.19771460.140512991445100
3.1923-4.0210.15241440.124812911435100
4.021-34.56350.14991380.14371283142199

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