+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43727 | |||||||||
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Title | Cryo-EM structure of BTV virion | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bluetongue virus / capsid protein / assembly intermediate / virion / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral genome replication / clathrin-dependent endocytosis of virus by host cell / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding Similarity search - Function | |||||||||
Biological species | Bluetongue virus (serotype 1 / isolate South Africa) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 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_43727.map.gz | 193 MB | EMDB map data format | |
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Header (meta data) | emd-43727-v30.xml emd-43727.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
Images | emd_43727.png | 181.8 KB | ||
Filedesc metadata | emd-43727.cif.gz | 8.3 KB | ||
Others | emd_43727_half_map_1.map.gz emd_43727_half_map_2.map.gz | 170.1 MB 170.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43727 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43727 | HTTPS FTP |
-Validation report
Summary document | emd_43727_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_43727_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_43727_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_43727_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43727 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43727 | HTTPS FTP |
-Related structure data
Related structure data | 8w1oMC 8w12C 8w19C 8w1cC 8w1iC 8w1rC 8w1sC 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_43727.map.gz / Format: CCP4 / Size: 216 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: #2
File | emd_43727_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_43727_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: #1-#5 / NCBI-ID: 10905 Sci species name: Bluetongue virus (serotype 1 / isolate South Africa) Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Ovis aries (sheep) |
Virus shell | Shell ID: 1 / Diameter: 880.0 Å |
-Macromolecule #1: Core protein VP3
Macromolecule | Name: Core protein VP3 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Molecular weight | Theoretical: 103.410508 KDa |
Sequence | String: MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSIS FRHIVMQSRD RVLRVDTYYE EMSQVGDVIT EDEPEKFYST IIKKVRFIRG KGSFILHDIP TRDHRGMEVA E PEVLGVEF ...String: MAAQNEQRPE RIKTTPYLEG DVLSSDSGPL LSVFALQEIM QKVRQVQADY MTATREVDFT VPDVQKILDD IKALAAEQVY KIVKVPSIS FRHIVMQSRD RVLRVDTYYE EMSQVGDVIT EDEPEKFYST IIKKVRFIRG KGSFILHDIP TRDHRGMEVA E PEVLGVEF KNVLPVLTAE HRAMIQNALD GSIIENGNVA TRDVDVFIGA CSEPVYRIYN RLQGYIEAVQ LQELRNSIGW LE RLGHRKR ITYSQEVLTD FRRQDTIWVL ALQLPVNPQV VWDVPRSSIA NLIMNIATCL PTGEYIAPNP RISSITLTQR ITT TGPFAI LTGSTPTAQQ LNDVRKIYLA LMFPGQIILD LKIDPGERMD PAVRMVAGVV GHLLFTAGGR FTNLTQNMAR QLDI ALNDY LLYMYNTRVQ VNYGPTGEPL DFQIGRNQYD CNVFRADFAT GTGYNGWATI DVEYREPAPY VHAQRYIRYC GIDSR ELIN PTTYGIGMTY HCYNEMLRML VAAGKDSEAA YFRSMLPFHM VRFARINQII NEDLHSVFSL PDDMFNALLP DLIAGA HQN ADPVVLDVSW ISLWFAFNRS FEPTHRNEML EVAPLIESVY ASELSVMKVD MRHLSLMQRR FPDVLIQARP SHFWKAV LN DSPEAVKAVM NLSHSHNFIN IRDMMRWVML PSLQPSLKLA LEEEAWAAAN DFEDLMLTDQ VYMHRDMLPE PRLDDIER F RQEGFYYTNM LEAPPEIDRV VQYTYEIARL QANMGQFRAA LRRIMDDDDW VRFGGVLRTV RVKFYDARPP DDVLQGLPF SYDTNERGGL AYATIKYATE TTIFYLIYNV EFSNTPDSLV LINPTYTMTK VFINKRIVER VRVGQILAVL NRRFVAYKGK MRIMDITQS LKMGTKLAAP TV UniProtKB: Core protein VP3 |
-Macromolecule #2: RNA-directed RNA polymerase
Macromolecule | Name: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Molecular weight | Theoretical: 149.926281 KDa |
Sequence | String: MVAITVQGAQ LIKRVVERFY PGIAFNINEG ACYIYKFSDH IRRIRMKHGT KYRRQAEEII RNISLRKERL YGIPVLDEVE WKYVFDGQT FQSYAFEVYV NSILPWSELD PEEEFLRNYR VSREMTEVEK FIEFRAKNEM QIYGDIPIKV WCCFINELSA E LKHVPLGM ...String: MVAITVQGAQ LIKRVVERFY PGIAFNINEG ACYIYKFSDH IRRIRMKHGT KYRRQAEEII RNISLRKERL YGIPVLDEVE WKYVFDGQT FQSYAFEVYV NSILPWSELD PEEEFLRNYR VSREMTEVEK FIEFRAKNEM QIYGDIPIKV WCCFINELSA E LKHVPLGM QVMADFVNRF DSPFHQGNRD LSNLEDFQVA YTTPLLFEMC CMESILEFNI KMRMREEEIS ALEFGDMKVD PV GLLREFF ILCLPHPKKI NNVLRAPYSW FVKMWGVGAD PIVVLQSTAG DDRNSKDVFY DKFRTEPNRY KALFRSSFYN ESR RMNEEK ILEAVKYSQK LGSHDRRLPL FEKMLKTVYT TPFYPHKSSN MILASFLLSI QTITGYGRAW VKNVSTEFDK QLKP NPSNL VQDVSDLTRE FFKQAYVEAK ERREEIVKPE DLYTSMLRLA RNTSSGFSTE IYVKKRFGPR LRDKDLIKIN SRIKA LVIF TKGHTVFTDE ELHKKYNSVE LYQTKGSRDV PIKATRTIYS INLSVLVPQL IVTLPLNEYF SRVGGITSPD YKKIGG KVI VGDLEATGSR VMDAADCFRN SADRDIFTIA IDYSEYDTHL TRHNFRTGML QGIREAMAPY RDLRYEGYTL EQIIDFG YG EGRVANTLWN GKRRLFKTTF DAYIRLDESE RDKGSFKVPK GVLPVSSVDV ANRIAVDKGF DTLIAATDGS DLALIDTH L SGENSTLIAN SMHNMAIGTL MQREVGREQP GVLTFLSEQY VGDDTLFYTK LHTTDTKVFD KVAASIFDTV AKCGHEASP SKTMMTPYSV EKTQTHAKQG CYVPQDRMMI ISSERRKDIE DVQGYVRSQV QTMITKVSRG FCHDLAQLIL MLKTTFIGAW KMKRTIKED AMYRDRKFDS NDEDGFTLIQ IRNPLALYVP IGWNGYGAHP AALNIVMTEE MYVDSIMISK LDEIMAPIRR I VHDIPPCW NETQGDKRGL ISATKMSFFS KMARPAVQAA LSDPQIINLV EELPLGEFSP GRISRTMMHS ALLKESSART LL SSGYELE YQKALNSWIT QVSMRLGEES GVISTSYAKL FDVYFEGELD GAPHMFPDQN LSPQFYIQKM MIGPRVSSRV RNS YVDRID VILRKDVVMR GFITANTILN VIEKLGTNHS VGDLVTVFTL MNIETRVAEE LAEYMTSEKI RFDALKLLKK GIAG DEFTM SLNVATQDFI DTYLAYPYQL TKTEVDAISL YCTQMIMLRA ALGLPKKKMK IVVTDDAKKR YKIRLQRFRT HVPKI KVLK KLIDPNRMTV RNLENQFV UniProtKB: RNA-directed RNA polymerase |
-Macromolecule #5: Outer capsid protein VP2
Macromolecule | Name: Outer capsid protein VP2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Molecular weight | Theoretical: 112.125461 KDa |
Sequence | String: MDELGIPVYK RGFPEHLLRG YEFIIDVGTK IESVGGRHDV TKIPEMNAYD IKQESIRTAL WYNPIRNDGF VLPRVLDITL RGYDERRAV VESTRHKSFH TNDQWVQWMM KDSMDAQPLK VGLDDQSRNV AHSLHNCVVK IDSKKADTMS YHVEPIEDAS K GCLHTRTM ...String: MDELGIPVYK RGFPEHLLRG YEFIIDVGTK IESVGGRHDV TKIPEMNAYD IKQESIRTAL WYNPIRNDGF VLPRVLDITL RGYDERRAV VESTRHKSFH TNDQWVQWMM KDSMDAQPLK VGLDDQSRNV AHSLHNCVVK IDSKKADTMS YHVEPIEDAS K GCLHTRTM MWNHLVRIET FHAAQEVAYT LKPTYDIVVH AERRDRSQPF RPGDQTLINF GRGQKVTMNH NSYDKMVEGL AH LVIRGKI PEVIRDDIAS LDEICNRWIQ SRHDPGEIKA YELCKILSTI GRKVLDREKE PEDEASLSIR FQEAIDNKFR QHD PERLKI FEHRNQRRDE DRFYILLMIA ASDTFNTRVW WSNPYPCLRG TLIASETKLG DVYSMMRSWY DWSVRPTYTP YEKT REQEK YIYGRVNLFD FVAEPGIKIV HWEYRLNHST REITYAQGNP CDLYPEDDDV IVTKFDDVAY GQMINEMING GWNQE QFKM HKILKSEGNV LTIDFEKDAK LTTNEGVTMP EYFNKWIIAP MFNAKLRIKH EEIAQRQSDD PMVKRTLSPI TADPIE LQR LTLARFYDIR PALRGQALSR QQAQSTYDEE ISKRQDYAEI LKRRGIVQIP KKPCPTVTAQ YTLERYALFI ISILQQH VV RDCDEEAVYE HPKADHELEI FGESIVDISQ VIILAFDLIF ERRRRVRDVY ESRHIIARIR RMRGKERLNV IAEFFPTY G GLLNGLNSAT VVQNIMYLNF LPLYFLVGDN MIYSHRQWSI PLLLYTHEVM VVPLEVGSYN DRCGLIAYLE YMVFFPSKA IRFSKLNEAQ PKIAREMLKY YANTTVYDGG VNYNVVTTKQ LLYETYLASL CGGISDGIVW YLPITHPNKC IVAIEVSDER VPASIRAGR IRLRFPLSAR HLKGVVIIQI DEEGEFTVYS EGIVSHRVCK KNLLKYMCDI ILLKFSGHVF GNDEMLTKLL N V UniProtKB: Outer capsid protein VP2 |
-Macromolecule #3: RNA-1
Macromolecule | Name: RNA-1 / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Molecular weight | Theoretical: 2.167323 KDa |
Sequence | String: UAUUAAU |
-Macromolecule #4: RNA-2
Macromolecule | Name: RNA-2 / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Bluetongue virus (serotype 1 / isolate South Africa) |
Molecular weight | Theoretical: 2.825735 KDa |
Sequence | String: UAUUAAUAA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.8 / Component - Concentration: 20.0 mM / Component - Name: Tris |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / 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 | Virus isolated from infected BHK cells |
-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: 3 / Number real images: 62928 / 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: 81 |
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Output model | PDB-8w1o: |