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- EMDB-9687: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-9687
TitleCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Map data
SampleCryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
  • (Capsid protein ...Capsid) x 4
  • IgG receptor FcRn large subunit p51
  • Beta-2-microglobulinBeta-2 microglobulin
  • (ligand) x 3
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 ferrous iron binding / positive regulation of transferrin receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / regulation of membrane depolarization / negative regulation of receptor binding / regulation of erythrocyte differentiation / MHC class I peptide loading complex / 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
Immunoglobulin-like fold / MHC class I-like antigen recognition-like superfamily / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin-like domain / MHC class I-like antigen recognition-like / MHC classes I/II-like antigen recognition protein / Beta-2-Microglobulin / Immunoglobulin-like domain superfamily
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin
Biological speciesEchovirus E6 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao GF / Liu S / Zhao X / Peng R
Funding support China, 1 items
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 ReportPDB-ID: 6ilm

SummaryFull reportAbout validation report
History
DepositionOct 19, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ilm
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ilm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9687.png

Downloads & links

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Map

FileDownload / File: emd_9687.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.097 / Movie #1: 0.06
Minimum - Maximum-0.19409378 - 0.31763908
Average (Standard dev.)0.0016758248 (±0.017399272)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1940.3180.002

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Supplemental data

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Sample components

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Entire Cryo-EM structure of Echovirus 6 complexed with its uncoating rec...

EntireName: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Number of components: 10

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Component #1: protein, Cryo-EM structure of Echovirus 6 complexed with its unco...

ProteinName: Cryo-EM structure of Echovirus 6 complexed with its uncoating receptor FcRn at PH 7.4
Recombinant expression: No
SourceSpecies: Echovirus E6

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Component #2: protein, Capsid protein VP1

ProteinName: Capsid protein VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.968648 kDa
SourceSpecies: Echovirus E6

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Component #3: protein, Capsid protein VP2

ProteinName: Capsid protein VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.06452 kDa
SourceSpecies: Echovirus E6

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Component #4: protein, Capsid protein VP3

ProteinName: Capsid protein VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.378936 kDa
SourceSpecies: Echovirus E6

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Component #5: protein, Capsid protein VP4

ProteinName: Capsid protein VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.338014 kDa
SourceSpecies: Echovirus E6

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Component #6: protein, IgG receptor FcRn large subunit p51

ProteinName: IgG receptor FcRn large subunit p51 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.294971 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Beta-2-microglobulin

ProteinName: Beta-2-microglobulinBeta-2 microglobulin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.74816 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, SPHINGOSINE

LigandName: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299492 kDa

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Component #9: ligand, POTASSIUM ION

LigandName: POTASSIUM IONPotassium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

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Component #10: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 26153
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

6ilm

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