[English] 日本語
Yorodumi
- EMDB-22897: Disulfide Stabilized Norovirus GI.1 VLP Shell Region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22897
TitleDisulfide Stabilized Norovirus GI.1 VLP Shell Region
Map dataSharpened map
Sample
  • Virus: Norovirus Hu/1968/US
    • Protein or peptide: Capsid protein VP1
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesNorwalk virus (strain GI/Human/United States/Norwalk/1968) / Norovirus Hu/1968/US
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsGorman J / Kwong PD
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD019994-01 United States
Other privateSF349247 (Simons Foundation) United States
Other privateF00316 (Agouron Institute) United States
CitationJournal: NPJ Vaccines / Year: 2020
Title: Disulfide stabilization of human norovirus GI.1 virus-like particles focuses immune response toward blockade epitopes.
Authors: Raffaello Verardi / Lisa C Lindesmith / Yaroslav Tsybovsky / Jason Gorman / Gwo-Yu Chuang / Caitlin E Edwards / Paul D Brewer-Jensen / Michael L Mallory / Li Ou / Arne Schön / Wei Shi / Ena ...Authors: Raffaello Verardi / Lisa C Lindesmith / Yaroslav Tsybovsky / Jason Gorman / Gwo-Yu Chuang / Caitlin E Edwards / Paul D Brewer-Jensen / Michael L Mallory / Li Ou / Arne Schön / Wei Shi / Ena S Tully / George Georgiou / Ralph S Baric / Peter D Kwong /
Abstract: Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has ...Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has been shown to be safe and highly immunogenic, but its efficacy and durability have been limited. Here, we show that norovirus GI.1 VLPs are unstable and contain a substantial fraction of dissociated VLP components. Broadly reactive, non-neutralizing antibodies isolated from vaccinated donors bound to the dissociated components, but not to the intact VLPs. Engineering of interprotomer disulfide bonds within the shell domain prevented disassembly of the VLPs, while preserving antibody accessibility to blockade epitopes. Without adjuvant, mice immunized with stabilized GI.1 VLPs developed faster blockade antibody titers compared to immunization with wild-type GI.1 VLPs. In addition, immunization with stabilized particles focused immune responses toward surface-exposed epitopes and away from occluded epitopes. Overall, disulfide-stabilized norovirus GI.1 VLPs elicited improved responses over the non-disulfide-stabilized version, suggesting their promise as candidate vaccines.
History
DepositionOct 26, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.303511221
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.303511221
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kjp
  • Surface level: 0.303511221
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kjp
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22897.png

Downloads & links

-
Map

FileDownload / File: emd_22897.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.07325 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3035112
Minimum - Maximum-0.76244336 - 1.734595
Average (Standard dev.)0.015537479 (±0.064476445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 643.95 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073251.073251.07325
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z643.950643.950643.950
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.7621.7350.016

-
Supplemental data

-
Mask #1

Fileemd_22897_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map

Fileemd_22897_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_22897_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_22897_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Norovirus Hu/1968/US

EntireName: Norovirus Hu/1968/US
Components
  • Virus: Norovirus Hu/1968/US
    • Protein or peptide: Capsid protein VP1

-
Supramolecule #1: Norovirus Hu/1968/US

SupramoleculeName: Norovirus Hu/1968/US / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 524364 / Sci species name: Norovirus Hu/1968/US / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Strain: GI/Human/United States/Norwalk/1968
Molecular weightTheoretical: 56.664961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGCAFT AGKIIVSCIP PGFGSHNLTI AQATLFPHVI ADVRTLDPIE V PLEDVRNV ...String:
MMMASKDATS SVDGASGAGQ LVPEVNASDP LAMDPVAGSS TAVATAGQVN PIDPWIINNF VQAPQGEFTI SPNNTPGDVL FDLSLGPHL NPFLLHLSQM YNGWVGNMRV RIMLAGCAFT AGKIIVSCIP PGFGSHNLTI AQATLFPHVI ADVRTLDPIE V PLEDVRNV LFHNNDRNQQ TMRLVCMLYT PLRTCGGTGD SFVVAGRVMT CPSPDFNFLF LVPPTVEQKT RPFTLPNLPL SS LSNSRAP LPISSMGISP DNVQSVQFQN GRCTLDGRLV GTTPVSLSHV AKIRGTSNGT VINLTELDGT PFHPFEGPAP IGF PDLGGC DWHINMTQFG HSSQTQYDVD TTPDTFVPHL GSIQANGIGS GNYVGVLSWI SPPSHPSGSQ VDLWKIPNYG SSIT EATHL APSVYPPGFG EVLVFFMSKM PGPGAYNLPC LLPQEYISHL ASEQAPTVGE AALLHYVDPD TGRNLGEFKA YPDGF LTCV PNGASSGPQQ LPINGVFVFV SWVSRFYQLK PVGTASSARG RLGLRR

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Component - Name: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 777 / Average electron dose: 70.48 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 23476

-
Atomic model buiding 1

Initial modelPDB ID:

1ihm

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7kjp:
Disulfide Stabilized Norovirus GI.1 VLP Shell Region

+
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