[English] 日本語
Yorodumi
- EMDB-23960: Norovirus T=3 GII.4 HOV VLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23960
TitleNorovirus T=3 GII.4 HOV VLP
Map data
Sample
  • Virus: Norovirus GII.4
    • Protein or peptide: VP1
  • Ligand: water
KeywordsT=3 Capsid GII.4 HOV Norovirus / VIRUS
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1
Function and homology information
Biological speciesNorovirus GII.4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSalmen W / Hu L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057788 United States
CitationJournal: Nat Commun / Year: 2022
Title: Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity.
Authors: Liya Hu / Wilhelm Salmen / Rong Chen / Yi Zhou / Frederick Neill / James E Crowe / Robert L Atmar / Mary K Estes / B V Venkataram Prasad /
Abstract: Human noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being ...Human noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being used in vaccine development. The atomic structure of the GII.4 capsid in the native T = 3 state has not been determined. Here we present the GII.4 VLP structure with T = 3 symmetry determined using X-ray crystallography and cryo-EM at 3.0 Å and 3.8 Å resolution, respectively, which reveals unanticipated novel features. A novel aspect in the crystal structure determined without imposing icosahedral symmetry is the remarkable adaptability of the capsid protein VP1 driven by the flexible hinge between the shell and the protruding domains. In both crystal and cryo-EM structures, VP1 adopts a stable conformation with the protruding domain resting on the shell domain, in contrast to the 'rising' conformation observed in recent cryo-EM structures of other GII.4 VLPs. Our studies further revealed that the resting state of VP1 dimer is stabilized by a divalent ion, and chelation using EDTA increases capsid diameter, exposing new hydrophobic and antigenic sites and suggesting a transition to the rising conformation. These novel insights into GII.4 capsid structure, stability, and antigen presentation may be useful for ongoing vaccine development.
History
DepositionMay 10, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.653
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.653
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7mry
  • Surface level: 0.653
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7mry
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23960.png

Downloads & links

-
Map

FileDownload / File: emd_23960.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 500 pix.
= 620. Å		1.24 Å/pix.
x 500 pix.
= 620. Å		1.24 Å/pix.
x 500 pix.
= 620. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6528 / Movie #1: 0.653
Minimum - Maximum-1.5675443 - 2.5133166
Average (Standard dev.)0.015316859 (±0.1321882)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 620.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z620.000620.000620.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-1.5682.5130.015

-
Supplemental data

-
Mask #1

Fileemd_23960_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_23960_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_23960_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Norovirus GII.4

EntireName: Norovirus GII.4
Components
  • Virus: Norovirus GII.4
    • Protein or peptide: VP1
  • Ligand: water

-
Supramolecule #1: Norovirus GII.4

SupramoleculeName: Norovirus GII.4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 489821 / Sci species name: Norovirus GII.4 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

-
Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Norovirus GII.4
Molecular weightTheoretical: 58.760895 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKMASSDASP SDGSTANLVP EVNNEVMALE PVVGAAIAAP VAGQQNVIDP WIRNNFVQAP GGEFTVSPRN APGEILWSAP LGPDLNPYL SHLARMYNGY AGGFEVQVIL AGNAFTAGKI IFAAVPPNFP TEGLSPSQVT MFPHIIVDVR QLEPVLIPLP D VRNNFYHY ...String:
MKMASSDASP SDGSTANLVP EVNNEVMALE PVVGAAIAAP VAGQQNVIDP WIRNNFVQAP GGEFTVSPRN APGEILWSAP LGPDLNPYL SHLARMYNGY AGGFEVQVIL AGNAFTAGKI IFAAVPPNFP TEGLSPSQVT MFPHIIVDVR QLEPVLIPLP D VRNNFYHY NQSNDPTIKL IAMLYTPLRA NNAGDDVFTV SCRVLTRPSP DFDFIFLVPP TVESRTKPFT VPILTVEEMT NS RFPIPLE KLFTGPSGAF VVQPQNGRCT TDGVLLGTTQ LSPVNICTFR GDVTHIAGTH DYTMNLASQN WNNYDPTEEI PAP LGTPDF VGKIQGVLTQ TTRGDGSTRG HKATVSTGSV HFTPKLGSVQ FTTDTNNDLE TGQNTKFTPV GVVQDGNSAH QNEP QQWVL PNYSGRTGHN VHLAPAVAPT FPGEQLLFFR STMPGCSGYP NMNLDCLLPQ EWVLHFYQEA APAQSDVALL RFVNP DTGR VLFECKLHKS GYVTVAHTGP HDLVIPPNGY FRFDSWVNQF YTLAPMGNGA GRRRAL

UniProtKB: VP1

-
Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.96 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 55.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0)
Details: Using Cryosparc GSFSC, resolution calculated: No Mask = 4.2 A, Spherical = 4 A, Loose = 3.9 A, Tight = 3.8 A, corrected = 3.8 A
Number images used: 51913
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.15.0)

+
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