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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


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
SourceEchovirus E6 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGao GF / Liu S / Zhao X / Peng R
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 FG
Validation ReportPDB-ID: 6ilm

SummaryFull reportAbout validation report
DateDeposition: Oct 19, 2018 / Header (metadata) release: May 15, 2019 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

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

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
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
start NX/NY/NZ000
NX/NY/NZ208208208
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

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