+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43714 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of VP3-VP6 heterohexamer | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Bluetongue virus / capsid protein / heterohexamer / VIRAL PROTEIN | |||||||||
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 / Core protein VP3 / VP6 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
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_43714.map.gz | 56.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-43714-v30.xml emd-43714.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_43714.png | 203 KB | ||
Filedesc metadata | emd-43714.cif.gz | 6.8 KB | ||
Others | emd_43714_half_map_1.map.gz emd_43714_half_map_2.map.gz | 48.5 MB 48.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43714 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43714 | HTTPS FTP |
-Validation report
Summary document | emd_43714_validation.pdf.gz | 796.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_43714_full_validation.pdf.gz | 795.6 KB | Display | |
Data in XML | emd_43714_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_43714_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43714 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43714 | HTTPS FTP |
-Related structure data
Related structure data | 8w12MC 8w19C 8w1cC 8w1iC 8w1oC 8w1rC 8w1sC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_43714.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_43714_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_43714_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Bluetongue virus (serotype 1 / isolate South Africa)
Entire | Name: Bluetongue virus (serotype 1 / isolate South Africa) |
---|---|
Components |
|
-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 |
---|---|
Host (natural) | Organism: Ovis aries (sheep) |
Molecular weight | Theoretical: 460 KDa |
-Macromolecule #1: Core protein VP3
Macromolecule | Name: Core protein VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) Strain: BTV1 |
Molecular weight | Theoretical: 105.613969 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAHHHHHHSS GLEVLFQGPG MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILD DIKALAAEQV YKIVKVPSIS FRHIVMQSRD RVLRVDTYYE EMSQVGDVIT EDEPEKFYST IIKKVRFIRG K GSFILHDI ...String: MAHHHHHHSS GLEVLFQGPG MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILD DIKALAAEQV YKIVKVPSIS FRHIVMQSRD RVLRVDTYYE EMSQVGDVIT EDEPEKFYST IIKKVRFIRG K GSFILHDI PTRDHRGMEV AEPEVLGVEF KNVLPVLTAE HRAMIQNALD GSIIENGNVA TRDVDVFIGA CSEPVYRIYN RL QGYIEAV QLQELRNSIG WLERLGHRKR ITYSQEVLTD FRRQDTIWVL ALQLPVNPQV VWDVPRSSIA NLIMNIATCL PTG EYIAPN PRISSITLTQ RITTTGPFAI LTGSTPTAQQ LNDVRKIYLA LMFPGQIILD LKIDPGERMD PAVRMVAGVV GHLL FTAGG RFTNLTQNMA RQLDIALNDY LLYMYNTRVQ VNYGPTGEPL DFQIGRNQYD CNVFRADFAT GTGYNGWATI DVEYR EPAP YVHAQRYIRY CGIDSRELIN PTTYGIGMTY HCYNEMLRML VAAGKDSEAA YFRSMLPFHM VRFARINQII NEDLHS VFS LPDDMFNALL PDLIAGAHQN ADPVVLDVSW ISLWFAFNRS FEPTHRNEML EVAPLIESVY ASELSVMKVD MRHLSLM QR RFPDVLIQAR PSHFWKAVLN DSPEAVKAVM NLSHSHNFIN IRDMMRWVML PSLQPSLKLA LEEEAWAAAN DFEDLMLT D QVYMHRDMLP EPRLDDIERF RQEGFYYTNM LEAPPEIDRV VQYTYEIARL QANMGQFRAA LRRIMDDDDW VRFGGVLRT VRVKFYDARP PDDVLQGLPF SYDTNERGGL AYATIKYATE TTIFYLIYNV EFSNTPDSLV LINPTYTMTK VFINKRIVER VRVGQILAV LNRRFVAYKG KMRIMDITQS LKMGTKLAAP TV UniProtKB: Core protein VP3 |
-Macromolecule #2: VP6
Macromolecule | Name: VP6 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) Strain: BTV1 |
Molecular weight | Theoretical: 22.5655 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSAAMLLAPG DVIKRSSEEL KQRQIQINLI DWTEGESEKE SKAEAKEGDK AEELKDGEGT QSERDLRRKE KSGAHAKAAE RGRRKQGKK PHGDAQREGT EEEKTSEEPA SVGITIEGVM SQKKLLSMIG GVERKMAPIG ARESAVMLVS NSIKDVVRAT A YFTAPTGD ...String: MSAAMLLAPG DVIKRSSEEL KQRQIQINLI DWTEGESEKE SKAEAKEGDK AEELKDGEGT QSERDLRRKE KSGAHAKAAE RGRRKQGKK PHGDAQREGT EEEKTSEEPA SVGITIEGVM SQKKLLSMIG GVERKMAPIG ARESAVMLVS NSIKDVVRAT A YFTAPTGD PHWKEVAREA SKKKNILAYT STGGDVKTEF LHLIDHL UniProtKB: VP6, VP6 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||
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 | Recombinated VP3-VP6 complex purified from insect cell |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: 2843 / 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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 107 |
---|---|
Output model | PDB-8w12: |