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- PDB-6ilm: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec... -

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Entry
Database: PDB / ID: 6ilm
TitleCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Components
  • (Capsid protein ...Capsid) x 4
  • Beta-2-microglobulinBeta-2 microglobulin
  • IgG receptor FcRn large subunit p51
KeywordsVIRUS / Echovirus 6 / FcRn / Cryo-EM / virus-receptor complex
Function / homology
Function and homology information


Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / Amyloid fiber formation / Interferon gamma signaling / Neutrophil degranulation ...Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / Amyloid fiber formation / Interferon gamma signaling / Neutrophil degranulation / IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / early endosome lumen / regulation of membrane depolarization / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / ER to Golgi transport vesicle membrane / regulation of defense response to virus by virus / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / cellular response to iron(III) ion / negative regulation of receptor binding / recycling endosome membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I protein complex / HFE-transferrin receptor complex / positive regulation of T cell mediated cytotoxicity / response to molecule of bacterial origin / positive regulation of T cell cytokine production / cellular response to iron ion / positive regulation of receptor binding / phagocytic vesicle membrane / positive regulation of receptor-mediated endocytosis / interferon-gamma-mediated signaling pathway / retina homeostasis / T cell differentiation in thymus / specific granule lumen / early endosome membrane / iron ion homeostasis / iron ion transport / negative regulation of neuron projection development / response to cadmium ion / antibacterial humoral response / regulation of immune response / tertiary granule lumen / positive regulation of protein binding / antimicrobial humoral immune response mediated by antimicrobial peptide / protein refolding / immune response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / response to drug / Golgi membrane / external side of plasma membrane / endoplasmic reticulum lumen / focal adhesion / innate immune response / cellular protein metabolic process / neutrophil degranulation / Golgi apparatus / extracellular space / extracellular exosome / membrane / integral component of membrane / extracellular region / identical protein binding / plasma membrane / cytosol
Beta-2-Microglobulin / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / MHC class I-like antigen recognition-like superfamily / Immunoglobulin-like domain / MHC class I-like antigen recognition-like / Ig-like domain profile. ...Beta-2-Microglobulin / Immunoglobulin C1-set domain / Immunoglobulin-like domain superfamily / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / MHC class I-like antigen recognition-like superfamily / Immunoglobulin-like domain / MHC class I-like antigen recognition-like / Ig-like domain profile. / Immunoglobulin-like fold / MHC classes I/II-like antigen recognition protein / Immunoglobulins and major histocompatibility complex proteins signature.
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Specimen sourceHomo sapiens (human)
Echovirus E6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao, G.F. / Liu, S. / Zhao, X. / Peng, R.
Funding supportChina , 1件
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000China
CitationJournal: To Be Published
Title: structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Authors: Liu, S. / Peng, R. / Zhao, X. / George, F.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2018 / Release: May 15, 2019Array

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1559
Polymers135,7936
Non-polymers3623
Water0
1
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,169,290540
Polymers8,147,595360
Non-polymers21,695180
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 5


  • icosahedral pentamer
  • 681 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)680,77445
Polymers678,96630
Non-polymers1,80815
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein VP1
B: Capsid protein VP2
C: Capsid protein VP3
D: Capsid protein VP4
E: IgG receptor FcRn large subunit p51
F: Beta-2-microglobulin
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 817 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)816,92954
Polymers814,75936
Non-polymers2,16918
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Capsid protein ... , 4 types, 4 molecules ABCD

#1: Protein/peptide Capsid protein VP1 /


Mass: 32968.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#2: Protein/peptide Capsid protein VP2 /


Mass: 28064.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#3: Protein/peptide Capsid protein VP3 /


Mass: 26378.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#4: Protein/peptide Capsid protein VP4 /


Mass: 7338.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6

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Protein/peptide , 2 types, 2 molecules EF

#5: Protein/peptide IgG receptor FcRn large subunit p51 / FcRn / Neonatal Fc receptor


Mass: 29294.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCRN / Cell (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P55899
#6: Protein/peptide Beta-2-microglobulin / Beta-2 microglobulin / FcRn light chain


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P61769

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Non-polymers , 3 types, 3 molecules

#7: Chemical ChemComp-SPH / SPHINGOSINE


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Sphingosine
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Potassium
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Sodium

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Details

Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MH830353.1 FOR THE PROTEIN.

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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

ComponentName: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6 / Source: MULTIPLE SOURCES
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)

Entity assembly-ID: 1

IDOrganismNcbi tax-ID
2Echovirus E612062
3Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26153 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.0039789
f_angle_d0.75513328
f_dihedral_angle_d8.4235786
f_chiral_restr0.0521442
f_plane_restr0.0071735

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