[English] 日本語
Yorodumi
- EMDB-10128: Thermally-stabilised mutant murine norovirus (MNV-1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10128
TitleThermally-stabilised mutant murine norovirus (MNV-1)
Map dataEM density map for heat-stable mutant (hs)MNV, filtered by local resolution.
Sample
  • Virus: Murine norovirus 1
    • Protein or peptide: Heat-stable mutant murine norovirus (MNV-1) VP1
Biological speciesMurine norovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSnowden JS / Hurdiss DL / Adeyemi OO / Ranson NA / Herod MR / Stonehouse NJ
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust102174/B/13/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007229/1 United Kingdom
Wellcome Trust102572/B/13/Z United Kingdom
CitationJournal: PLoS Biol / Year: 2020
Title: Dynamics in the murine norovirus capsid revealed by high-resolution cryo-EM.
Authors: Joseph S Snowden / Daniel L Hurdiss / Oluwapelumi O Adeyemi / Neil A Ranson / Morgan R Herod / Nicola J Stonehouse /
Abstract: Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically ...Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically challenging yet could be key for developing rational therapeutic agents to combat infections. Noroviruses are nonenveloped, icosahedral viruses of global importance to human health. They are a common cause of acute gastroenteritis, yet no vaccines or specific antiviral agents are available. Here, we use genetics and cryo-electron microscopy (cryo-EM) to study the high-resolution solution structures of murine norovirus as a model for human viruses. By comparing our 3 structures (at 2.9- to 3.1-Å resolution), we show that whilst there is little change to the shell domain of the capsid, the radiating protruding domains are flexible, adopting distinct states both independently and synchronously. In doing so, the capsids sample a range of conformational space, with implications for maintaining virion stability and infectivity.
History
DepositionJul 16, 2019-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateJun 3, 2020-
Current statusJun 3, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0326
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0326
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10128.png

Downloads & links

-
Map

FileDownload / File: emd_10128.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map for heat-stable mutant (hs)MNV, filtered by local resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 500 pix.
= 532.5 Å		1.07 Å/pix.
x 500 pix.
= 532.5 Å		1.07 Å/pix.
x 500 pix.
= 532.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0326 / Movie #1: 0.0326
Minimum - Maximum-0.3420231 - 0.5409905
Average (Standard dev.)0.0019286736 (±0.021223577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 532.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z532.500532.500532.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.3420.5410.002

-
Supplemental data

-
Mask #1

Fileemd_10128_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Sharpened density map.

Fileemd_10128_additional_1.map
AnnotationSharpened density map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened density map from 3D refinement.

Fileemd_10128_additional_2.map
AnnotationUnsharpened density map from 3D refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: First half map from 3D refinement.

Fileemd_10128_half_map_1.map
AnnotationFirst half map from 3D refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Second half map from 3D refinement.

Fileemd_10128_half_map_2.map
AnnotationSecond half map from 3D refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Murine norovirus 1

EntireName: Murine norovirus 1
Components
  • Virus: Murine norovirus 1
    • Protein or peptide: Heat-stable mutant murine norovirus (MNV-1) VP1

-
Supramolecule #1: Murine norovirus 1

SupramoleculeName: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: RAW264.7 cells / NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Sci species strain: CW1P3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus musculus (house mouse)
Host systemOrganism: Murine norovirus 1 / Recombinant strain: CW1P3
Virus shellShell ID: 1 / T number (triangulation number): 3

-
Macromolecule #1: Heat-stable mutant murine norovirus (MNV-1) VP1

MacromoleculeName: Heat-stable mutant murine norovirus (MNV-1) VP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1 / Strain: CW1P3
Recombinant expressionOrganism: Murine norovirus 1
SequenceString: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP LLDVRRVLWH ...String:
MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP LLDVRRVLWH ATQDQEESMR LVCMLYTPLR TNSPGDESFV VSGRLLSKPA ADFNFVYLTP PIERTIYRMV DLPVIQPRLC THARWPAPVY GLLVDPSLPS NPQWQNGRVH VDGTLLGTTP ISGSWVSCFA AEAAYEFQSG TGEVATFTLI EQDGSAYVPG DRAAPLGYPD FSGQLEIEVQ TETTKTGDKL KVTTFEMILG PTTNADQAPY QGRVFASVTA AASLDLVDGR VRAVPRSIYG FQDTIPEYND GQLVPLAPPI GPFLPGEVLL RFRTYMRQID TADAAAEAID CALPQEFVSW FASNAFTVQS EALLLRYRNT LTGQLLFECK LYNEGYIALS YSGSGPLTFP TDGIFEVVSW VPRLYQLASV GSLATGRMLK Q

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
5.0 mMMgCl2Magnesium chloride
1.0 mMKClPotassium chloride
1.0 mMCaCl2Calcium chloride
10.0 mMC8H18N2O4SHEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER / Details: RELION initial model generation.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35263
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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