+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8734 | |||||||||
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Title | Electron cryo-microscopy of "immature" Chikungunya VLP | |||||||||
Map data | Chikungunya virus strain Senegal 37997 | |||||||||
Sample |
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Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / membrane => GO:0016020 / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Chikungunya virus strain Senegal 37997 / Chikungunya virus (strain 37997) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Rossmann MG / Yap ML | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Structural studies of Chikungunya virus maturation. Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann / Abstract: Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. ...Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-Å resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8734.map.gz | 249 MB | EMDB map data format | |
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Header (meta data) | emd-8734-v30.xml emd-8734.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8734_fsc.xml | 27.2 KB | Display | FSC data file |
Images | emd_8734.png | 270.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8734 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8734 | HTTPS FTP |
-Related structure data
Related structure data | 5vu2MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8734.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Chikungunya virus strain Senegal 37997 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-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 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host system | Organism: Homo sapiens (human) / Recombinant cell: Human embryonic kidney / Recombinant plasmid: pUC119 |
-Macromolecule #1: E1 envelope glycoprotein
Macromolecule | Name: E1 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997 |
Molecular weight | Theoretical: 95.538164 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: STKDNFNVYK ATRPYLAHCP DCGEGHSCHS PVALERIRNE ATDGTLKIQV SLQIGIKTDD SHDWTKLRYM DNHMPADAER AGLFVRTSA PCTITGTMGH FILARCPKGE TLTVGFTDSR KISHSCTHPF HHDPPVIGRE KFHSRPQHGK ELPCSTYVQS T AATTEEIE ...String: STKDNFNVYK ATRPYLAHCP DCGEGHSCHS PVALERIRNE ATDGTLKIQV SLQIGIKTDD SHDWTKLRYM DNHMPADAER AGLFVRTSA PCTITGTMGH FILARCPKGE TLTVGFTDSR KISHSCTHPF HHDPPVIGRE KFHSRPQHGK ELPCSTYVQS T AATTEEIE VHMPPDTPDR TLMSQQSGNV KITVNGQTVR YKCNCGGSNE GLTTTDKVIN NCKVDQCHAA VTNHKKWQYN SP LVPRNAE LGDRKGKIHI PFPLANVTCR VPKARNPTVT YGKNQVIMLL YPDHPTLLSY RNMGEEPNYQ EEWVMHKKEV VLT VPTEGL EVTWGNNEPY KYWPQLSTNG TAHGHPHEII LYYYELYPTM TVVVVSVATF ILLSMVGMAA GMCMCARRRC ITPY ELTPG ATVPFLLSLI CCIRTAKAAT YQEAAIYLWN EQQPLFWLQA LIPLAALIVL CNCLRLLPCC CKTLAFLAVM SVGAH TVSA YEHVTVIPNT VGVPYKTLVN RPGYSPMVLE MELLSVTLEP TLSLDYITCE YKTVIPSPYV KCCGTAECKD KNLPDY SCK VFTGVYPFMW GGAYCFCDAE NTQLSEAHVE KSESCKTEFA SAYRAHTASA SAKLRVLYQG NNITVTAYAN GDHAVTV KD AKFIVGPMSS AWTPFDNKIV VYKGDVYNMD YPPFGAGRPG QFGDIQSRTP ESKDVYANTQ LVLQRPAAGT VHVPYSQA P SGFKYWLKER GASLQHTAPF GCQIATNPVR AVNCAVGNMP ISIDIPEAAF TRVVDAPSLT DMSCEVPACT HSSDFGGVA IIKYAASKKG KCAVHSMTNA VTIREAEIEV EGNSQLQISF STALASAEFR VQVCSTQVHC AAECHP |
-Macromolecule #2: E3 envelope glycoprotein
Macromolecule | Name: E3 envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997 |
Molecular weight | Theoretical: 6.92699 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: PVMCLLANTT FPCSQPPCTP CCYEKEPEET LRMLEDNVMR PGYYQLLQAS LTCSPHRQRE |
-Macromolecule #3: capsid protein
Macromolecule | Name: capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus (strain 37997) / Strain: 37997 |
Molecular weight | Theoretical: 16.229508 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: CIFEVKHEGK VMGYACLVGD KVMKPAHVKG TIDNADLAKL AFKRSSKYDL ECAQIPVHMK SDASKFTHEK PEGYYNWHHG AVQYSGGRF TIPTGAGKPG DSGRPIFDNK GRVVAIVLGG ANEGARTALS VVTWNKDIVT KITPEGAEEW |
-Macromolecule #4: E1 envelope glycoprotein
Macromolecule | Name: E1 envelope glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997 |
Molecular weight | Theoretical: 4.810723 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: HTTLGVQDIS TTAMSWVQKI TGGVGLIVAV AALILIVVLC VSFSRH |
-Macromolecule #5: E2 envelope glycoprotein
Macromolecule | Name: E2 envelope glycoprotein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus strain Senegal 37997 / Strain: 37997 |
Molecular weight | Theoretical: 8.817458 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: STNGTAHGHP HEIILYYYEL YPTMTVVIVS VASFVLLSMV GTAVGMCVCA RRRCITPYEL TPGATVPFLL SLLCCVRTTK A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 36.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |