[English] 日本語
Yorodumi
- EMDB-20202: Asymmetric focsued reconstruction of human norovirus GII.2 Snow M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20202
TitleAsymmetric focsued reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP asymmetric unit in T=1 symmetry
Map dataAsymmetric focused reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP asymmetric unit in T=1 symmetry
Sample
  • Virus: Snow Mountain virus
    • Protein or peptide: Viral protein 1
  • Ligand: ZINC ION
  • Ligand: water
KeywordsCaliciviridae / Norovirus / GII.2 / Snow Mountain Virus / VIRUS LIKE PARTICLE
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Viral protein 1
Function and homology information
Biological speciesSnow Mountain virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsJung J / Grant T
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations.
Authors: James Jung / Timothy Grant / Dennis R Thomas / Chris W Diehnelt / Nikolaus Grigorieff / Leemor Joshua-Tor /
Abstract: Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available ...Noroviruses are a leading cause of foodborne illnesses worldwide. Although GII.4 strains have been responsible for most norovirus outbreaks, the assembled virus shell structures have been available in detail for only a single strain (GI.1). We present high-resolution (2.6- to 4.1-Å) cryoelectron microscopy (cryo-EM) structures of GII.4, GII.2, GI.7, and GI.1 human norovirus outbreak strain virus-like particles (VLPs). Although norovirus VLPs have been thought to exist in a single-sized assembly, our structures reveal polymorphism between and within genogroups, with small, medium, and large particle sizes observed. Using asymmetric reconstruction, we were able to resolve a Zn metal ion adjacent to the coreceptor binding site, which affected the structural stability of the shell. Our structures serve as valuable templates for facilitating vaccine formulations.
History
DepositionMay 4, 2019-
Header (metadata) releaseMay 29, 2019-
Map releaseJun 26, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
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-6ouc
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20202.png

Downloads & links

-
Map

FileDownload / File: emd_20202.map.gz / Format: CCP4 / Size: 10 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric focused reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP asymmetric unit in T=1 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 107 pix.
= 114.49 Å		1.07 Å/pix.
x 102 pix.
= 109.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.6177347 - 1.0704243
Average (Standard dev.)-0.00057097385 (±0.04100011)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions107102240
Spacing102107240
CellA: 109.14001 Å / B: 114.490005 Å / C: 256.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z102107240
origin x/y/z0.0000.0000.000
length x/y/z109.140114.490256.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS102107240
D min/max/mean-0.6181.070-0.001

-
Supplemental data

-
Sample components

-
Entire : Snow Mountain virus

EntireName: Snow Mountain virus
Components
  • Virus: Snow Mountain virus
    • Protein or peptide: Viral protein 1
  • Ligand: ZINC ION
  • Ligand: water

-
Supramolecule #1: Snow Mountain virus

SupramoleculeName: Snow Mountain virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 52276 / Sci species name: Snow Mountain virus / Sci species strain: GII.2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.56 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 310.0 Å / T number (triangulation number): 1

-
Macromolecule #1: Viral protein 1

MacromoleculeName: Viral protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Snow Mountain virus
Molecular weightTheoretical: 59.321809 KDa
Recombinant expressionOrganism: Nicotiana (plant)
SequenceString: MKMASNDAAP STDGAAGLVP ESNNEVMALE PVAGAALAAP VTGQTNIIDP WIRANFVQAP NGEFTVSPRN APGEVLLNLE LGPELNPYL AHLARMYNGY AGGMEVQVML AGNAFTAGKL VFAAVPPHFP VENLSPQQIT MFPHVIIDVR TLEPVLLPLP D VRNNFFHY ...String:
MKMASNDAAP STDGAAGLVP ESNNEVMALE PVAGAALAAP VTGQTNIIDP WIRANFVQAP NGEFTVSPRN APGEVLLNLE LGPELNPYL AHLARMYNGY AGGMEVQVML AGNAFTAGKL VFAAVPPHFP VENLSPQQIT MFPHVIIDVR TLEPVLLPLP D VRNNFFHY NQKDDPKMRI VAMLYTPLRS NGSGDDVFTV SCRVLTRPSP DFDFTYLVPP TVESKTKPFT LPILTLGELS NS RFPVSID QMYTSPNEVI SVQCQNGRCT LDGELQGTTQ LQVSGICAFK GEVTAHLQDN DHLYNITITN LNGSPFDPSE DIP APLGVP DFQGRVFGVI TQRDKQNAAG QSQPANRGHD AVVPTYTAQY TPKLGQVQIG TWQTDDLKVN QPVKFTPVGL NDTE HFNQW VVPRYAGALN LNTNLAPSVA PVFPGERLLF FRSYLPLKGG YGNPAIDCLL PQEWVQHFYQ EAAPSMSEVA LVRYI NPDT GRALFEAKLH RAGFMTVSSN TSAPVVVPAN GYFRFDSWVN QFYSLAPMGT GNGRRRIQ

UniProtKB: Viral protein 1

-
Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 124 / 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

Concentration4 mg/mL
BufferpH: 5.75
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2809 / Average exposure time: 7.0 sec. / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
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: 76405
Startup modelType of model: OTHER / Details: ab inito
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0)
Details: Symmetry expansion and signal subtraction of the icosahedral asymmetric units from the whole particle images, followed by asymmetric focused reconstruction towards the apex of the spike domain
Number images used: 1486080
Initial angle assignmentType: COMMON LINE / Software - Name: cisTEM (ver. 1.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4rpb


Chain - Chain ID: A / Chain - Residue range: 225-532 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6ouc:
Asymmetric focsued reconstruction of human norovirus GII.2 Snow Mountain Virus strain VLP asymmetric unit in T=1 symmetry

+
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