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

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Basic information

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


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / beta-2-microglobulin binding / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / early endosome lumen / antigen processing and presentation of peptide antigen via MHC class I / 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 ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / beta-2-microglobulin binding / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / early endosome lumen / antigen processing and presentation of peptide antigen via MHC class I / 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 transferrin receptor binding / positive regulation of ferrous iron binding / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / regulation of membrane depolarization / negative regulation of receptor binding / MHC class I peptide loading complex / regulation of erythrocyte differentiation / recycling endosome membrane / regulation of iron ion transport / MHC class I protein complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / cellular response to iron ion / positive regulation of T cell cytokine production / positive regulation of T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of receptor binding / negative regulation of neurogenesis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of receptor-mediated endocytosis / positive regulation of cellular senescence / specific granule lumen / modulation of age-related behavioral decline / retina homeostasis / negative regulation of epithelial cell proliferation / interferon-gamma-mediated signaling pathway / early endosome membrane / T cell differentiation in thymus / iron ion transport / negative regulation of neuron projection development / iron ion homeostasis / response to cadmium ion / amyloid fibril formation / regulation of immune response / tertiary granule lumen / antibacterial humoral response / protein homotetramerization / positive regulation of protein binding / protein refolding / endosome membrane / learning or memory / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / cellular response to lipopolysaccharide / defense response to Gram-positive bacterium / Golgi membrane / external side of plasma membrane / endoplasmic reticulum lumen / focal adhesion / cellular protein metabolic process / innate immune response / neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / membrane / integral component of membrane / extracellular region / identical protein binding / plasma membrane / cytosol
MHC class I-like antigen recognition-like / Immunoglobulin C1-set domain / Immunoglobulin-like fold / Beta-2-Microglobulin / Immunoglobulin-like domain superfamily / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin-like domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set ...MHC class I-like antigen recognition-like / Immunoglobulin C1-set domain / Immunoglobulin-like fold / Beta-2-Microglobulin / Immunoglobulin-like domain superfamily / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin-like domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Jelly Rolls - #20 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Beta-2-microglobulin / IgG receptor FcRn large subunit p51
Biological speciesHomo 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 support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010000 China
CitationJournal: Cell / Year: 2019
Title: Human Neonatal Fc Receptor Is the Cellular Uncoating Receptor for Enterovirus B.
Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / ...Authors: Xin Zhao / Guigen Zhang / Sheng Liu / Xiangpeng Chen / Ruchao Peng / Lianpan Dai / Xiao Qu / Shihua Li / Hao Song / Zhengrong Gao / Pengfei Yuan / Zhiheng Liu / Changyao Li / Zifang Shang / Yan Li / Meifan Zhang / Jianxun Qi / Han Wang / Ning Du / Yan Wu / Yuhai Bi / Shan Gao / Yi Shi / Jinghua Yan / Yong Zhang / Zhengde Xie / Wensheng Wei / George F Gao /
Abstract: Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for ...Enterovirus B (EV-B), a major proportion of the genus Enterovirus in the family Picornaviridae, is the causative agent of severe human infectious diseases. Although cellular receptors for coxsackievirus B in EV-B have been identified, receptors mediating virus entry, especially the uncoating process of echovirus and other EV-B remain obscure. Here, we found that human neonatal Fc receptor (FcRn) is the uncoating receptor for major EV-B. FcRn binds to the virus particles in the "canyon" through its FCGRT subunit. By obtaining multiple cryo-electron microscopy structures at different stages of virus entry at atomic or near-atomic resolution, we deciphered the underlying mechanisms of enterovirus attachment and uncoating. These structures revealed that different from the attachment receptor CD55, binding of FcRn to the virions induces efficient release of "pocket factor" under acidic conditions and initiates the conformational changes in viral particle, providing a structural basis for understanding the mechanisms of enterovirus entry.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 5, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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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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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 Capsid protein VP1 /


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


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


Mass: 26378.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E6
#4: Protein 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 , 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 (production host): 293T / Production host: Homo sapiens (human) / References: UniProt: P55899
#6: Protein 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 / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-K / POTASSIUM ION / Potassium


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION

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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)
IDEntity assembly-IDOrganismNcbi tax-ID
21Echovirus E612062
31Homo 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-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039789
ELECTRON MICROSCOPYf_angle_d0.75513328
ELECTRON MICROSCOPYf_dihedral_angle_d8.4235786
ELECTRON MICROSCOPYf_chiral_restr0.0521442
ELECTRON MICROSCOPYf_plane_restr0.0071735

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