[English] 日本語
Yorodumi
- EMDB-9053: CryoEM structure of human enterovirus D68 full native virion (pH ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9053
TitleCryoEM structure of human enterovirus D68 full native virion (pH 6.5, 4 degrees Celsius, 3 min)
Map datasharpened map in which the inner density is masked out
Sample
  • Virus: Enterovirus D68
    • Protein or peptide: Viral protein 1
    • Protein or peptide: Viral protein 2
    • Protein or peptide: Viral protein 3
    • Protein or peptide: Viral protein 4
Biological speciesEnterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLiu Y / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Molecular basis for the acid-initiated uncoating of human enterovirus D68.
Authors: Yue Liu / Ju Sheng / Arno L W van Vliet / Geeta Buda / Frank J M van Kuppeveld / Michael G Rossmann /
Abstract: Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes ...Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.
History
DepositionAug 27, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseDec 19, 2018-
UpdateJan 9, 2019-
Current statusJan 9, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 36.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 36.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9053.png

Downloads & links

-
Map

FileDownload / File: emd_9053.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map in which the inner density is masked out
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 264 pix.
= 456.72 Å		1.73 Å/pix.
x 264 pix.
= 456.72 Å		1.73 Å/pix.
x 264 pix.
= 456.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 36.399999999999999 / Movie #1: 36.4
Minimum - Maximum-161.80225999999999 - 229.856200000000001
Average (Standard dev.)0.54331374 (±14.357525000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions264264264
Spacing264264264
CellA=B=C: 456.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.731.731.73
M x/y/z264264264
origin x/y/z0.0000.0000.000
length x/y/z456.720456.720456.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS264264264
D min/max/mean-161.802229.8560.543

-
Supplemental data

-
Half map: unsharpened half map in which the inner density is retained

Fileemd_9053_half_map_1.map
Annotationunsharpened half map in which the inner density is retained
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: unsharpened half map in which the inner density is retained

Fileemd_9053_half_map_2.map
Annotationunsharpened half map in which the inner density is retained
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Enterovirus D68

EntireName: Enterovirus D68
Components
  • Virus: Enterovirus D68
    • Protein or peptide: Viral protein 1
    • Protein or peptide: Viral protein 2
    • Protein or peptide: Viral protein 3
    • Protein or peptide: Viral protein 4

-
Supramolecule #1: Enterovirus D68

SupramoleculeName: Enterovirus D68 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Viruses were grown in RD cells. / NCBI-ID: 42789 / Sci species name: Enterovirus D68 / Sci species strain: US/MO/14-18947 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Viral protein 1

MacromoleculeName: Viral protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSN TEP EEAIQTRTVI NQHGVSETLV ENFLSRAALV SKRSFEYKDH TSSTARADKN FFKWTIN TR SFVQLRRKLE LFTYLRFDAE ITILTTVAVN GSGNNTYVGL PDLTLQAMFV PTGALTPE K QDSFHWQSGS ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSN TEP EEAIQTRTVI NQHGVSETLV ENFLSRAALV SKRSFEYKDH TSSTARADKN FFKWTIN TR SFVQLRRKLE LFTYLRFDAE ITILTTVAVN GSGNNTYVGL PDLTLQAMFV PTGALTPE K QDSFHWQSGS NASVFFKISD PPARITIPFM CINSAYSVFY DGFAGFEKNG LYGINPADT IGNLCVRIVN EHQPVGFTVT VRVYMKPKHI KAWAPRPPRT LPYMSIANAN YKGKERAPNA LSAIIGNRD SVKTMPHNIV NT

-
Macromolecule #2: Viral protein 2

MacromoleculeName: Viral protein 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString: SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI D KPTQPETA TDRFYTLKSV KWETGSTGWW WKLPDALNNI GMFGQNVQHH YLYRSGFLIH VQ CNATKFH QGALLVVAIP EHQRGAHNTN TSPGFDDIMK GEEGGTFNHP YVLDDGTSLA CAT ...String:
SPSAEACGYS DRVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI D KPTQPETA TDRFYTLKSV KWETGSTGWW WKLPDALNNI GMFGQNVQHH YLYRSGFLIH VQ CNATKFH QGALLVVAIP EHQRGAHNTN TSPGFDDIMK GEEGGTFNHP YVLDDGTSLA CAT IFPHQW INLRTNNSAT IVLPWMNAAP MDFPLRHNQW TLAIIPVVPL GTRTTSSMVP ITVS IAPMC CEFNGLRHAI TQ

-
Macromolecule #3: Viral protein 3

MacromoleculeName: Viral protein 3 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNM LEVVQV ESMMEINNTE SAVGMERLKV DISALTDVDQ LLFNIPLDIQ LDGPLRNTLV GNIS RYYTH WSGSLEMTFM FCGSFMAAGK LILCYTPPGG SCPTTRETAM LGTHIVWDFG LQSSV TLII ...String:
GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNM LEVVQV ESMMEINNTE SAVGMERLKV DISALTDVDQ LLFNIPLDIQ LDGPLRNTLV GNIS RYYTH WSGSLEMTFM FCGSFMAAGK LILCYTPPGG SCPTTRETAM LGTHIVWDFG LQSSV TLII PWISGSHYRM FNNDAKSTNA NVGYVTCFMQ TNLIVPSESS DTCSLIGFIA AKDDFS LRL MRDSPDIGQL DHLHAAEAAY Q

-
Macromolecule #4: Viral protein 4

MacromoleculeName: Viral protein 4 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Enterovirus D68 / Strain: US/MO/14-18947
SequenceString:
GAQVTRQQTG THENANIATN GSHITYNQIN FYKDSYAASA SKQDFSQDPS KFTEPVVEG LKAGAPVLK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5 / Details: phosphate citrate buffer
GridMaterial: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 357 / Average exposure time: 10.5 sec. / Average electron dose: 28.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 39022
CTF correctionSoftware - Name: jspr
Details: On-the-fly CTF correction during 2D alignment and 3D reconstruction
Startup modelType of model: OTHER / Details: Particle orientations were randomly assigned.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 15000
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: jspr
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 0.5 degrees
Software - Name: jspr
Final 3D classificationSoftware - Name: RELION (ver. 2.1.0)
Details: 33863 particles were selected after 2D classification. Subsequently, 3D classification yielded full native virions, A-particles and expanded 1 particles.
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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