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- PDB-6e48: Crystal Structure of the Murine Norovirus VP1 P domain in complex... -

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Basic information

Entry
Database: PDB / ID: 6.0E+48
TitleCrystal Structure of the Murine Norovirus VP1 P domain in complex with the CD300lf Receptor and Lithocholic Acid
Components
  • CMRF35-like molecule 1
  • VP1 P domain
KeywordsVIRAL PROTEIN / Norovirus / Capsid protein / Protruding domain / bile acid / LCA / myeloid receptor / CMRF-35-like molecule-1 / CLM-1 / CLM1 / DIR2 / IREM1 / LMIR3 / PIGR3 / IgSF13
Function / homology
Function and homology information


negative regulation of MyD88-dependent toll-like receptor signaling pathway / interleukin-13-mediated 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 ...negative regulation of MyD88-dependent toll-like receptor signaling pathway / interleukin-13-mediated 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 / virion component / virus receptor activity / host cell cytoplasm / plasma membrane
Similarity search - Function
SHP2-interacting transmembrane adaptor protein, SIT / : / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 ...SHP2-interacting transmembrane adaptor protein, SIT / : / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CMRF35-like molecule 1 / Capsid protein VP1
Similarity search - Component
Biological speciesMurine norovirus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 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)AI127552 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109725 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
DepositionJul 16, 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
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1 P domain
B: VP1 P domain
F: CMRF35-like molecule 1
G: CMRF35-like molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,72913
Polymers91,6734
Non-polymers1,0569
Water20,3931132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-81 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.091, 152.891, 70.037
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ABFG

#1: Protein VP1 P domain / VP1


Mass: 33050.223 Da / Num. of mol.: 2 / Fragment: VP1 Protruding domain (UNP residues 229-532)
Source method: isolated from a genetically manipulated source
Details: native / Source: (gene. exp.) Murine norovirus 1 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q80J94
#2: 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: 12786.489 Da / Num. of mol.: 2 / Fragment: CD300lf ectodomain (UNP residues 20-131)
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Mus musculus (house mouse) / Gene: CD300lf, CLM1, DIR2, IREM1, LMIR3, PIGR3, IgSF13 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6SJQ7

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Non-polymers , 4 types, 1141 molecules

#3: Chemical ChemComp-4OA / (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid / Lithocholic acid


Mass: 376.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 0.1 M Tris, pH 8.7, 40 mM calcium chloride, 5.5% PEG10000

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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 2, 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: 1.8→63.68 Å / Num. obs: 95932 / % possible obs: 95 % / Redundancy: 2 % / CC1/2: 0.996 / Net I/σ(I): 5.92
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 11228 / CC1/2: 0.324 / % possible all: 63

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3LQ6 & 5FFL

3lq6

5ffl


Resolution: 1.801→63.674 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.2039 2552 2.66 %
Rwork0.1743 --
obs0.1751 95929 94.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.67 Å2 / Biso mean: 23.9946 Å2 / Biso min: 9.46 Å2
Refinement stepCycle: final / Resolution: 1.801→63.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6426 0 148 1132 7706
Biso mean--27.84 31.78 -
Num. residues----830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0226692
X-RAY DIFFRACTIONf_angle_d1.1099095
X-RAY DIFFRACTIONf_chiral_restr0.2741024
X-RAY DIFFRACTIONf_plane_restr0.0091173
X-RAY DIFFRACTIONf_dihedral_angle_d12.0663934
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8009-1.83550.3775770.34312807288452
1.8355-1.8730.37341130.32924140425377
1.873-1.91370.35071280.30084670479887
1.9137-1.95830.32051390.2675105524494
1.9583-2.00720.2891450.22915356550199
2.0072-2.06150.26881470.206753895536100
2.0615-2.12220.19671480.19754105558100
2.1222-2.19070.23161490.177154165565100
2.1907-2.2690.21151470.173454125559100
2.269-2.35980.18991490.157154355584100
2.3598-2.46720.21281510.154754335584100
2.4672-2.59730.16111480.155454685616100
2.5973-2.760.18461470.148954425589100
2.76-2.97310.20581520.157354815633100
2.9731-3.27230.17831490.152254975646100
3.2723-3.74580.19191520.147555415693100
3.7458-4.71910.13191520.129355715723100
4.7191-63.71360.19091590.187458045963100

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