+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28979 | |||||||||
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Title | Cryo-EM structure of Chikungunya virus asymmetric unit | |||||||||
Map data | chikv_asu_165.mrc | |||||||||
Sample |
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Keywords | CHIKV asymmetric unit / VIRUS | |||||||||
Function / homology | Function and homology information T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Chikungunya virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
Authors | Su GC / Chmielewsk D / 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_28979.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-28979-v30.xml emd-28979.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28979_fsc.xml | 24.5 KB | Display | FSC data file |
Images | emd_28979.png | 146 KB | ||
Filedesc metadata | emd-28979.cif.gz | 7.1 KB | ||
Others | emd_28979_half_map_1.map.gz emd_28979_half_map_2.map.gz | 146.4 MB 146.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28979 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28979 | HTTPS FTP |
-Related structure data
Related structure data | 8fcgMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28979.map.gz / Format: CCP4 / Size: 17.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | chikv_asu_165.mrc | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.352 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: run half2 class001 unfil.mrc
File | emd_28979_half_map_1.map | ||||||||||||
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Annotation | run_half2_class001_unfil.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: run half2 class001 unfil.mrc
File | emd_28979_half_map_2.map | ||||||||||||
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Annotation | run_half2_class001_unfil.mrc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chikungunya virus
Entire | Name: Chikungunya virus |
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Components |
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-Supramolecule #1: Chikungunya virus
Supramolecule | Name: Chikungunya virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 37124 / Sci species name: Chikungunya virus / Sci species strain: vaccine strain 181/clone 25 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Molecular weight | Theoretical: 500 KDa |
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 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin |
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Source (natural) | Organism: Chikungunya virus / Strain: vaccine strain 181/clone 25 |
Molecular weight | Theoretical: 47.497906 KDa |
Sequence | String: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS ...String: YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KSLPDYSCKV FTGVYPFMW GGAYCFCDTE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNVTVSAYAN GDHAVTVKDA K FIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESEDVYANTQ LVLQRPSAGT VHVPYSQAPS GF KYWLKER GASLQHTAPF GCQIATNPVR AMNCAVGNMP ISIDIPDAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVAI IKY AASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHPPKDH IVNYPASHTT LGVQ DISVT AMSWVQKITG GVGLVVAVAA LILIVVLCVS FSRH UniProtKB: Structural polyprotein |
-Macromolecule #2: E2 glycoprotein
Macromolecule | Name: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin |
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Source (natural) | Organism: Chikungunya virus / Strain: vaccine strain 181/clone 25 |
Molecular weight | Theoretical: 47.077719 KDa |
Sequence | String: NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP ...String: NFNVYKAIRP YLAHCPDCGE GHSCHSPVAL ERIRNEATDG TLKIQVSLQI GIKTDDSHDW TKLRYMDNHM PADAERARLF VRTSAPCTI TGTMGHFILA RCPKGETLTV GFTDGRKISH SCTHPFHHDP PVIGREKFHS RPQHGRELPC STYAQSTAAT A EEIEVHMP PDTPDRTLMS QQSGNVKITV NSQTVRYKCN CGDSNEGLTT TDKVINNCKV DQCHAAVTNH KKWQYNSPLV PR NAELGDR KGKVHIPFPL ANVTCRVPKA RNPTVTYGKN QVIMLLYPDH PTLLSYRNMG EEPNYQEEWV THKKEIRLTV PTE GLEVTW GNNEPYKYWP QLSTNGTAHG HPHEIILYYY ELYPTMTVVV VSVASFVLLS MVGVAVGMCM CARRRCITPY ELTP GATVP FLLSLICCIR TAKA UniProtKB: Structural polyprotein |
-Macromolecule #3: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin |
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Source (natural) | Organism: Chikungunya virus / Strain: vaccine strain 181/clone 25 |
Molecular weight | Theoretical: 16.428607 KDa |
Sequence | String: NDCIFEVKHE GKVTGYACLV GDKVMKPAHV KGTIDNADLA KLAFKRSSKY DLECAQIPVH MKSDASKFTH EKPEGYYNWH HGAVQYSGG RFTIPTGAGK PGDSGRPIFD NKGRVVAIVL GGANEGARTA LSVVTWNKDI VTKITPEGAE EW UniProtKB: Structural polyprotein |
-Macromolecule #4: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: PCW |
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Molecular weight | Theoretical: 787.121 Da |
Chemical component information | ChemComp-PCW: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 106000 |
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: 47.25 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |