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- PDB-7b5f: Structure of echovirus 18 in complex with neonatal Fc receptor -

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Basic information

Entry
Database: PDB / ID: 7b5f
TitleStructure of echovirus 18 in complex with neonatal Fc receptor
Components
  • (Echovirus 18 viral protein ...) x 4
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
KeywordsVIRUS / complex / echovirus 18 virion / neonatal fc receptor / fcrn / beta-2-microglobulin / microglobulin / pocket factor
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / peptide antigen assembly with MHC class II protein complex / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / T=pseudo3 icosahedral viral capsid / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / host cell cytoplasmic vesicle membrane / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / nucleoside-triphosphate phosphatase / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / channel activity / protein refolding / early endosome membrane / monoatomic ion transmembrane transport / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / DNA replication / RNA helicase activity / endosome membrane / immune response / endocytosis involved in viral entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / symbiont-mediated activation of host autophagy / external side of plasma membrane / Golgi membrane / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / virion attachment to host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / ATP hydrolysis activity / proteolysis / extracellular space
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Picornavirus coat protein VP4 superfamily / Jelly Rolls - #20 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / MHC class I-like antigen recognition-like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / MHC class I-like antigen recognition-like superfamily / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / MHC classes I/II-like antigen recognition protein / Picornavirus/Calicivirus coat protein / : / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANINE / PALMITIC ACID / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Echovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBuchta, D. / Levdansky, Y. / Fuzik, T. / Mukhamedova, L. / Moravcova, J. / Hrebik, D. / Andersen, J.T. / Plevka, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
CitationJournal: To Be Published
Title: Structure of echovirus 18 in complex with neonatal Fc receptor
Authors: Buchta, D. / Levdansky, Y. / Fuzik, T. / Mukhamedova, L. / Moravcova, J. / Hrebik, D. / Andersen, J.T. / Plevka, P.
History
DepositionDec 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_struct_oper_list
Item: _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
C: Echovirus 18 viral protein 3
D: Echovirus 18 viral protein 4
A: Echovirus 18 viral protein 1
B: Echovirus 18 viral protein 2
G: IgG receptor FcRn large subunit p51
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8628
Polymers136,4546
Non-polymers4082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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Echovirus 18 viral protein ... , 4 types, 4 molecules CDAB

#1: Protein Echovirus 18 viral protein 3


Mass: 26143.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Tissue: Kidney
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Echovirus 18 viral protein 4


Mass: 7475.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Organ: Kidney
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Echovirus 18 viral protein 1


Mass: 32564.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Tissue: Kidney
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Echovirus 18 viral protein 2


Mass: 28802.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / Tissue: Kidney
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Protein , 2 types, 2 molecules GH

#5: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 29720.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Cell line (production host): High Five cells / Production host: unidentified baculovirus / References: UniProt: P55899
#6: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): High Five cells / Production host: unidentified baculovirus / References: UniProt: P61769

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Non-polymers , 2 types, 2 molecules

#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of echovirus 18 in complex with neonatal Fc receptorCOMPLEX#1-#60MULTIPLE SOURCES
2Echovirus 18 native virionCOMPLEX#1-#41NATURAL
3Heterodimer of neonatal Fc Receptor and beta-2-microglobulinCOMPLEX#5-#61RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
1110.12 MDaNO
217.63 MDaNO
312.49 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Echovirus E1847506
23Homo sapiens (human)9606
Source (recombinant)Organism: unidentified baculovirus
Natural hostOrganism: homo sapiens / Strain: echovirus 18
Buffer solutionpH: 7.3
Details: Mixed in 1:1 volume ratio {20 mM Tris (pH=7.2), 100 mM NaCl} and {8 mM Na2HPO4, 2 mM KH2PO4 (pH=7.4), 137 mM NaCl, 2.7 mM KCl}=PBS
Buffer component
IDConc.NameFormulaBuffer-ID
110 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris1
2118.5 mMsodium chlorideNaCl1
31.35 mMpotassium chlorideKCl1
44 mMDisodium phosphateNa2HPO41
51 mMMonopotassium phosphateKH2PO41
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.27 sec. / Electron dose: 54.48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 4531 / Details: Images were collected in movie-mode at 50 frames.
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: (1.13_2992: ???) / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 125031
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13062 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingMethod: flexible fit / Target criteria: R-factors
RefinementResolution: 2.9→233.42 Å / SU ML: 0.65 / σ(F): 0.13 / Phase error: 34.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3108 36801 4.99 %
Rwork0.3084 --
obs0.3085 738078 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00638470
ELECTRON MICROSCOPYf_angle_d0.82652420
ELECTRON MICROSCOPYf_dihedral_angle_d20.00713705
ELECTRON MICROSCOPYf_chiral_restr0.165795
ELECTRON MICROSCOPYf_plane_restr0.0056715

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