[English] 日本語
Yorodumi
- EMDB-9687: Cryo-EM structure of Echovirus 6 complexed with its uncoating rec... -

+
Open data


ID or keywords:

Loading...

no data

-
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

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9687.png

Downloads & links

-
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
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

-
Supplemental data

-
Sample components

+
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

+
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

+
Component #2: protein, Capsid protein VP1

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

+
Component #3: protein, Capsid protein VP2

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

+
Component #4: protein, Capsid protein VP3

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

+
Component #5: protein, Capsid protein VP4

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

+
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)

+
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)

+
Component #8: ligand, SPHINGOSINE

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

+
Component #9: ligand, POTASSIUM ION

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

+
Component #10: ligand, SODIUM ION

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

-
Experimental details

-
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 %

-
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)

-
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)

-
Atomic model buiding

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

6ilm

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more