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Yorodumi- EMDB-43722: Cryo-EM structure of pre-subcore from in vitro assembled particles -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43722 | |||||||||
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Title | Cryo-EM structure of pre-subcore from in vitro assembled particles | |||||||||
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Sample |
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Keywords | Bluetongue virus / capsid protein / assembly intermediate / virial proteins / VIRUS LIKE PARTICLE | |||||||||
Function / homology | VP6 blue-tongue virus inner capsid protein / Orbivirus helicase VP6 / Inner layer core protein VP3, Orbivirus / Orbivirus VP3 (T2) protein / Inner layer core protein VP3, Reovirus / viral capsid / structural molecule activity / VP6 / Core protein VP3 Function and homology information | |||||||||
Biological species | Bluetongue virus (serotype 1 / isolate South Africa) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Xia X / Sung PY / Martynowycz MW / Gonen T / Roy P / Zhou ZH | |||||||||
Funding support | United States, United Kingdom, 2 items
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Citation | Journal: Cell / Year: 2024 Title: RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells. Authors: Xian Xia / Po-Yu Sung / Michael W Martynowycz / Tamir Gonen / Polly Roy / Z Hong Zhou / Abstract: Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques ...Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8 Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43722.map.gz | 110.6 MB | EMDB map data format | |
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Header (meta data) | emd-43722-v30.xml emd-43722.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_43722.png | 65.7 KB | ||
Filedesc metadata | emd-43722.cif.gz | 6.1 KB | ||
Others | emd_43722_half_map_1.map.gz emd_43722_half_map_2.map.gz | 97.8 MB 97.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43722 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43722 | HTTPS FTP |
-Validation report
Summary document | emd_43722_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_43722_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_43722_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_43722_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43722 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43722 | HTTPS FTP |
-Related structure data
Related structure data | 8w12C 8w19C 8w1cC 8w1iC 8w1oC 8w1rC 8w1sC 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_43722.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43722_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43722_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bluetongue virus (serotype 1 / isolate South Africa)
Entire | Name: Bluetongue virus (serotype 1 / isolate South Africa) |
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Components |
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-Supramolecule #1: Bluetongue virus (serotype 1 / isolate South Africa)
Supramolecule | Name: Bluetongue virus (serotype 1 / isolate South Africa) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10905 Sci species name: Bluetongue virus (serotype 1 / isolate South Africa) Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Ovis aries (sheep) |
-Macromolecule #1: inner capsid protein VP3
Macromolecule | Name: inner capsid protein VP3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSISF RHIVMQSRDR VLRVDTYYEE MSQVGDVITE DEPEKFYSTI IKKVRFIRGK GSFILHDIPT RDHRGMEVAE PEVLGVEFKN ...String: MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSISF RHIVMQSRDR VLRVDTYYEE MSQVGDVITE DEPEKFYSTI IKKVRFIRGK GSFILHDIPT RDHRGMEVAE PEVLGVEFKN VLPVLTAEHR AMIQNALDGS IIENGNVATR DVDVFIGACS EPVYRIYNRL QGYIEAVQLQ ELRNSIGWLE RLGHRKRITY SQEVLTDFRR QDTIWVLALQ LPVNPQVVWD VPRSSIANLI MNIATCLPTG EYIAPNPRIS SITLTQRITT TGPFAILTGS TPTAQQLNDV RKIYLALMFP GQIILDLKID PGERMDPAVR MVAGVVGHLL FTAGGRFTNL TQNMARQLDI ALNDYLLYMY NTRVQVNYGP TGEPLDFQIG RNQYDCNVFR ADFATGTGYN GWATIDVEYR EPAPYVHAQR YIRYCGIDSR ELINPTTYGI GMTYHCYNEM LRMLVAAGKD SEAAYFRSML PFHMVRFARI NQIINEDLHS VFSLPDDMFN ALLPDLIAGA HQNADPVVLD VSWISLWFAF NRSFEPTHRN EMLEVAPLIE SVYASELSVM KVDMRHLSLM QRRFPDVLIQ ARPSHFWKAV LNDSPEAVKA VMNLSHSHNF INIRDMMRWV MLPSLQPSLK LALEEEAWAA ANDFEDLMLT DQVYMHRDML PEPRLDDIER FRQEGFYYTN MLEAPPEIDR VVQYTYEIAR LQANMGQFRA ALRRIMDDDD WVRFGGVLRT VRVKFYDARP PDDVLQGLPF SYDTNERGGL AYATIKYATE TTIFYLIYNV EFSNTPDSLV LINPTYTMTK VFINKRIVER VRVGQILAVL NRRFVAYKGK MRIMDITQSL KMGTKLAAPT V UniProtKB: Core protein VP3 |
-Macromolecule #2: inner capsid protein VP6
Macromolecule | Name: inner capsid protein VP6 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Sequence | String: MSAAMLLAPG DVIKRSSEEL KQRQIQINLI DWTEGESEKE SKAEAKEGDK AEELKDGEGT QSESSQKKES SKETKDADVD RRIHTAVGSG SSAKGPGERA NENVDRGDGK VGGGGGDADA GVGATGANGG RWVVLTEEIA RAIESKYGTK IDVYRDEVPA QIIEVERSLQ ...String: MSAAMLLAPG DVIKRSSEEL KQRQIQINLI DWTEGESEKE SKAEAKEGDK AEELKDGEGT QSESSQKKES SKETKDADVD RRIHTAVGSG SSAKGPGERA NENVDRGDGK VGGGGGDADA GVGATGANGG RWVVLTEEIA RAIESKYGTK IDVYRDEVPA QIIEVERSLQ KELGISREGV AEQTERLRDL RRKEKSGAHA KAAERGRRKQ GKKPHGDAQR EGTEEEKTSE EPASVGITIE GVMSQKKLLS MIGGVERKMA PIGARESAVM LVSNSIKDVV RATAYFTAPT GDPHWKEVAR EASKKKNILA YTSTGGDVKT EFLHLIDHL UniProtKB: VP6 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | In vitro assembled capsid by using the purified proteins |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9015 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |