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- PDB-6la6: Cryo-EM structure of echovirus 11 complexed with its uncoating re... -

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Basic information

Entry
Database: PDB / ID: 6la6
TitleCryo-EM structure of echovirus 11 complexed with its uncoating receptor FcRn at pH 7.4
Components
  • (Capsid protein ...) x 4
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
KeywordsVIRUS / Cryo-EM structure / echovirus 11 / FcRn
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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion ...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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont genome entry into host cell via pore formation in plasma membrane / peptide antigen assembly with MHC class II protein complex / picornain 3C / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / T=pseudo3 icosahedral viral capsid / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / host cell cytoplasmic vesicle membrane / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / host cell / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / channel activity / ER-Phagosome pathway / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / symbiont-mediated suppression of host gene expression / Golgi membrane / symbiont-mediated activation of host autophagy / lysosomal membrane / external side of plasma 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 / symbiont entry into host cell / 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 / 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) ...Picornavirus coat protein VP4 superfamily / 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 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / 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 / 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 / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Echovirus E11
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsLiu, S. / Gao, F.G.
CitationJournal: Chin.Sci.Bull. / Year: 2020
Title: Molecular and structural basis of Echovirus 11 infection by using the dual-receptor system of CD55 and FcRn.
Authors: Niu, S. / Liu, C. / Liu, C. / Liu, S. / Song, Y. / Zhang, Y. / Tian, W. / Zhao, X. / Wang, P. / Gao, F.G.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Oct 7, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2020Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
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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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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


Theoretical massNumber of molelcules
Total (without water)134,8476
Polymers134,8476
Non-polymers00
Water00
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
x 60


Theoretical massNumber of molelcules
Total (without water)8,090,807360
Polymers8,090,807360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area25090 Å2
ΔGint-111 kcal/mol
Surface area53160 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
x 5


  • icosahedral pentamer
  • 674 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)674,23430
Polymers674,23430
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
x 6


  • icosahedral 23 hexamer
  • 809 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)809,08136
Polymers809,08136
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 Capsid protein VP1


Mass: 32277.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: Q2LJ73*PLUS
#2: Protein Capsid protein VP2


Mass: 27968.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: A0A0R5YS56*PLUS
#3: Protein Capsid protein VP3


Mass: 26062.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: A0A346I7K2*PLUS
#4: Protein Capsid protein VP4


Mass: 7495.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E11 / References: UniProt: E0WN77*PLUS

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Protein , 2 types, 2 molecules EF

#5: Protein 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 line (production host): HEK293T / Production host: Homo sapiens (human) / 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 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P61769

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Details

Has protein modificationY

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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
1Echovirus E11 complexed with its uncoating receptorCOMPLEXall0MULTIPLE SOURCES
2echovirus 11VIRUS#1-#41NATURAL
3FcRn receptorCOMPLEX#5-#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Echovirus E1112078
33Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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
Image recordingElectron dose: 1.025 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92892 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039689
ELECTRON MICROSCOPYf_angle_d0.55713195
ELECTRON MICROSCOPYf_dihedral_angle_d9.915732
ELECTRON MICROSCOPYf_chiral_restr0.0441432
ELECTRON MICROSCOPYf_plane_restr0.0051712

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