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Yorodumi- EMDB-41096: Cryo-electron tomography of Chikungunya virus pentamer structure -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41096 | |||||||||
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Title | Cryo-electron tomography of Chikungunya virus pentamer structure | |||||||||
Map data | Subtomogram average of one penton | |||||||||
Sample |
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Keywords | subtomogram average / alphavirus / in situ / VIRUS | |||||||||
Biological species | Chikungunya virus strain Senegal 37997 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | Chmielewsk D / Su GC / Kaelber J / Pintilie G / Chen M / Jin J / Auguste A / Chiu W | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41096.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-41096-v30.xml emd-41096.xml | 23.1 KB 23.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41096_fsc.xml | 6.7 KB | Display | FSC data file |
Images | emd_41096.png | 137.2 KB | ||
Filedesc metadata | emd-41096.cif.gz | 5.5 KB | ||
Others | emd_41096_additional_1.map.gz emd_41096_additional_2.map.gz emd_41096_additional_3.map.gz emd_41096_half_map_1.map.gz emd_41096_half_map_2.map.gz | 25.1 MB 25.2 MB 25.1 MB 14.4 MB 14.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41096 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41096 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41096.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Subtomogram average of one penton | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.72 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Focused classification of full capsid, class 0.
File | emd_41096_additional_1.map | ||||||||||||
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Annotation | Focused classification of full capsid, class 0. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused classification of full capsid, class 1.
File | emd_41096_additional_2.map | ||||||||||||
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Annotation | Focused classification of full capsid, class 1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused classification of full capsid, class 2.
File | emd_41096_additional_3.map | ||||||||||||
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Annotation | Focused classification of full capsid, class 2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map - even
File | emd_41096_half_map_1.map | ||||||||||||
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Annotation | Half map - even | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map - odd
File | emd_41096_half_map_2.map | ||||||||||||
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Annotation | Half map - odd | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chikungunya virus strain Senegal 37997
Entire | Name: Chikungunya virus strain Senegal 37997 |
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Components |
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-Supramolecule #1: Chikungunya virus strain Senegal 37997
Supramolecule | Name: 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 |
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Virus shell | Shell ID: 1 / Diameter: 700.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: E1 glycoprotein
Macromolecule | Name: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Sequence | String: 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
Macromolecule | Name: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Sequence | String: 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
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Sequence | String: NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGGR FTIPTGAGKP GDSGRPIFDN KGRVVAIVLG GANEGARTAL SVVTWNKDIV TKITPEGAEE W |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.5 µm / Nominal defocus min: 3.0 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.35 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |