[English] 日本語
Yorodumi
- EMDB-41096: Cryo-electron tomography of Chikungunya virus pentamer structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41096
TitleCryo-electron tomography of Chikungunya virus pentamer structure
Map dataSubtomogram average of one penton
Sample
  • Virus: Chikungunya virus strain Senegal 37997
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid protein
Keywordssubtomogram average / alphavirus / in situ / VIRUS
Biological speciesChikungunya virus strain Senegal 37997
Methodsubtomogram averaging / cryo EM / Resolution: 7.2 Å
AuthorsChmielewsk D / Su GC / Kaelber J / Pintilie G / Chen M / Jin J / Auguste A / Chiu W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P41GM103832 United States
CitationJournal: PNAS Nexus / Year: 2024
Title: Cryogenic electron microscopy and tomography reveal imperfect icosahedral symmetry in alphaviruses.
Authors: David Chmielewski / Guan-Chin Su / Jason T Kaelber / Grigore D Pintilie / Muyuan Chen / Jing Jin / Albert J Auguste / Wah Chiu /
Abstract: Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) ...Alphaviruses are spherical, enveloped RNA viruses with two-layered icosahedral architecture. The structures of many alphaviruses have been studied using cryogenic electron microscopy (cryo-EM) reconstructions, which impose icosahedral symmetry on the viral particles. Using cryogenic electron tomography (cryo-ET), we revealed a polarized symmetry defect in the icosahedral lattice of Chikungunya virus (CHIKV) in situ, similar to the late budding particles, suggesting the inherent imperfect symmetry originates from the final pinch-off of assembled virions. We further demonstrated this imperfect symmetry is also present in in vitro purified CHIKV and Mayaro virus, another arthritogenic alphavirus. We employed a subparticle-based single-particle analysis protocol to circumvent the icosahedral imperfection and boosted the resolution of the structure of the CHIKV to ∼3 Å resolution, which revealed detailed molecular interactions between glycoprotein E1-E2 heterodimers in the transmembrane region and multiple lipid-like pocket factors located in a highly conserved hydrophobic pocket. This complementary use of in situ cryo-ET and single-particle cryo-EM approaches provides a more precise structural description of near-icosahedral viruses and valuable insights to guide the development of structure-based antiviral therapies against alphaviruses.
History
DepositionJun 22, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41096.png

Downloads & links

-
Map

FileDownload / File: emd_41096.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of one penton
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 192 pix.
= 522.24 Å		2.72 Å/pix.
x 192 pix.
= 522.24 Å		2.72 Å/pix.
x 192 pix.
= 522.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-10.958796 - 13.266534999999999
Average (Standard dev.)0.008589829 (±0.91084427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 522.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Focused classification of full capsid, class 0.

Fileemd_41096_additional_1.map
AnnotationFocused classification of full capsid, class 0.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused classification of full capsid, class 1.

Fileemd_41096_additional_2.map
AnnotationFocused classification of full capsid, class 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Focused classification of full capsid, class 2.

Fileemd_41096_additional_3.map
AnnotationFocused classification of full capsid, class 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map - even

Fileemd_41096_half_map_1.map
AnnotationHalf map - even
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map - odd

Fileemd_41096_half_map_2.map
AnnotationHalf map - odd
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Chikungunya virus strain Senegal 37997

EntireName: Chikungunya virus strain Senegal 37997
Components
  • Virus: Chikungunya virus strain Senegal 37997
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid protein

-
Supramolecule #1: Chikungunya virus strain Senegal 37997

SupramoleculeName: Chikungunya virus strain Senegal 37997 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 371095 / Sci species name: Chikungunya virus strain Senegal 37997 / Sci species strain: vaccine strain 181/clone 25 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Diameter: 700.0 Å / T number (triangulation number): 4

-
Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMWG GAYCFCDTEN TQLSEAHVEK SESCKTEFAS AYRAHTASAS AKLRVLYQGN NVTVSAYANG DHAVTVKDAK FIVGPMSSAW ...String:
YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMWG GAYCFCDTEN TQLSEAHVEK SESCKTEFAS AYRAHTASAS AKLRVLYQGN NVTVSAYANG DHAVTVKDAK FIVGPMSSAW TPFDNKIVVY KGDVYNMDYP PFGAGRPGQF GDIQSRTPES EDVYANTQLV LQRPSAGTVH VPYSQAPSGF KYWLKERGAS LQHTAPFGCQ IATNPVRAMN CAVGNMPISI DIPDAAFTRV VDAPSLTDMS CEVPACTHSS DFGGVAIIKY AASKKGKCAV HSMTNAVTIR EAEIEVEGNS QLQISFSTAL ASAEFRVQVC STQVHCAAEC HPPKDHIVNY PASHTTLGVQ DISVTAMSWV QKITGGVGLV VAVAALILIV VLCVSFSRH

-
Macromolecule #2: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTIT GTMGHFILAR CPKGETLTVG FTDGRKISHS CTHPFHHDPP VIGREKFHSR PQHGRELPCS TYAQSTAATA EEIEVHMPPD ...String:
NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTIT GTMGHFILAR CPKGETLTVG FTDGRKISHS CTHPFHHDPP VIGREKFHSR PQHGRELPCS TYAQSTAATA EEIEVHMPPD TPDRTLMSQQ SGNVKITVNS QTVRYKCNCG DSNEGLTTTD KVINNCKVDQ CHAAVTNHKK WQYNSPLVPR NAELGDRKGK VHIPFPLANV TCRVPKARNP TVTYGKNQVI MLLYPDHPTL LSYRNMGEEP NYQEEWVTHK KEIRLTVPTE GLEVTWGNNE PYKYWPQLST NGTAHGHPHE IILYYYELYP TMTVVVVSVA SFVLLSMVGV AVGMCMCARR RCITPYELTP GATVPFLLS LICCIRTAKA

-
Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString:
NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGGR FTIPTGAGKP GDSGRPIFDN KGRVVAIVLG GANEGARTAL SVVTWNKDIV TKITPEGAEE W

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.5 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN2 / Number subtomograms used: 848
ExtractionNumber tomograms: 66 / Number images used: 848 / Software - Name: EMAN2
Final 3D classificationSoftware - Name: EMAN2
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN2
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