+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36870 | |||||||||
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Title | Structure of full Banna virus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | reovirus / complex / capsid protein / VIRUS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Banna virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
Authors | Li Z / Cao S | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structures of Banna virus in multiple states reveal stepwise detachment of viral spikes. Authors: Zhiqiang Li / Han Xia / Guibo Rao / Yan Fu / Tingting Chong / Kexing Tian / Zhiming Yuan / Sheng Cao / Abstract: Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions- ...Banna virus (BAV) is the prototype Seadornavirus, a class of reoviruses for which there has been little structural study. Here, we report atomic cryo-EM structures of three states of BAV virions-surrounded by 120 spikes (full virions), 60 spikes (partial virions), or no spikes (cores). BAV cores are double-layered particles similar to the cores of other non-turreted reoviruses, except for an additional protein component in the outer capsid shell, VP10. VP10 was identified to be a cementing protein that plays a pivotal role in the assembly of BAV virions by directly interacting with VP2 (inner capsid), VP8 (outer capsid), and VP4 (spike). Viral spikes (VP4/VP9 heterohexamers) are situated on top of VP10 molecules in full or partial virions. Asymmetrical electrostatic interactions between VP10 monomers and VP4 trimers are disrupted by high pH treatment, which is thus a simple way to produce BAV cores. Low pH treatment of BAV virions removes only the flexible receptor binding protein VP9 and triggers significant conformational changes in the membrane penetration protein VP4. BAV virions adopt distinct spatial organization of their surface proteins compared with other well-studied reoviruses, suggesting that BAV may have a unique mechanism of penetration of cellular endomembranes. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36870.map.gz | 371 MB | EMDB map data format | |
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Header (meta data) | emd-36870-v30.xml emd-36870.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
Images | emd_36870.png | 169.8 KB | ||
Filedesc metadata | emd-36870.cif.gz | 7 KB | ||
Others | emd_36870_additional_1.map.gz emd_36870_half_map_1.map.gz emd_36870_half_map_2.map.gz | 192.6 MB 334.8 MB 334.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36870 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36870 | HTTPS FTP |
-Validation report
Summary document | emd_36870_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_36870_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_36870_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_36870_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36870 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36870 | HTTPS FTP |
-Related structure data
Related structure data | 8k42MC 8k43C 8k44C 8k49C 8k4aC 8w9pC 8w9qC 8w9rC 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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-Map
File | Download / File: emd_36870.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_36870_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36870_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36870_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Banna virus
Entire | Name: Banna virus |
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Components |
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-Supramolecule #1: Banna virus
Supramolecule | Name: Banna virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 77763 / Sci species name: Banna virus / Sci species strain: YN15-126-01 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 1 / Details: OR004519 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Banna virus |
Molecular weight | Theoretical: 108.031008 KDa |
Sequence | String: MPRKKDQVTK NDDGNQTSDV QTQDFKTAVQ PDTNTAQLIK TYSNPKQRGD KGEIIYDGGL SSKLADVVDK TTEPHNADGA VKDGRIAPV KLDLEKQKLD KLKLFETSPF DPLTIKNNQD VVDKLYATQS SSIQEVVPTK TFATELQFGV TSEDMAKIYG A VAAVSKNV ...String: MPRKKDQVTK NDDGNQTSDV QTQDFKTAVQ PDTNTAQLIK TYSNPKQRGD KGEIIYDGGL SSKLADVVDK TTEPHNADGA VKDGRIAPV KLDLEKQKLD KLKLFETSPF DPLTIKNNQD VVDKLYATQS SSIQEVVPTK TFATELQFGV TSEDMAKIYG A VAAVSKNV NSSVTYEVKR GTHELIKVPT IPHNLVLIQS DNGKHALIKE DLGQWPVETG ISLVNQAGVF AVQLANKLGI DK PFVLDAG SNYFTDTSFI DTRKYCTDGL SPREIQKALN RQRAYYDRPE LTISENKTLL SQSIIYPDAD GNDVSIIFSG AMS HAIFTY AQSQWNKNII KLDDYIREIT LTVPKQYRPR RFKEIEHTHG YVYRELNQGS LLPLVDANLK ESSSYYFKKL MSSI SNVPV DARTLQSATA ALAADTGQAV NRAQHVSMLT NRLTTANAPT VRAITVLTCM FKQFRIGMTY ALDPNIMDVA AATCM LLFR PAQSISDEQY RYCLQTMAVF LTNTTYDIVN NDTIDVLKMK LRNQGWPFVE RYNAVEIDMS VEPLRSPGQV GRYYNP FNI DPLTKKHVED RLEEFINQVQ VGRFRNASGN AVGTTLAAFL RACRDKTSAN WRGYSVLVSR YRSLIPNELF ESLRNIS GE YNINPQDEHS FFFALAQINA DDEFIGAIDK ESAEYLDEYA TLARDISNSL TLVKAAFGPL ERTSGSIINH ANNLNKVI N HVFADKPLIS ETMLKILTID GTTGKDGYRN WLDKLVGHNY PVYVEPVVNI MNFISARFVA DSSYFGYTNE IMIMPNHIN VPVDDRFGFR DSPFCTSLPR TIMGNDVRRI SYNVFSMMED IDDVISEGFI LYDAYFNFSY DIMTTDGVTR LKEDILIVTD TGNDIKPIH FYIYFENRND KKLRYESKMN VSYRLYIKTP ACLLPLSDYM RAQHDYVSPS SSRVYIKDPA VVYTRS UniProtKB: Vp2 |
-Macromolecule #2: VP8
Macromolecule | Name: VP8 / type: protein_or_peptide / ID: 2 / Details: OR004525 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Banna virus |
Molecular weight | Theoretical: 32.885305 KDa |
Sequence | String: MANRATSAFL DNPHPVGVNY VDEGSRQFVA VAELLASKLI DSSRESDESN SDVPFVQAYS KFADDNPRHL RVKTGGKMAN ALTNVIRSY YSINAPAIVP QVEIDRLASK ATVSGDMYNS YAIFNSVPIV EVLSPARTTV SIVGSDRADV TMLNTGAGAA N ITFNFGQI ...String: MANRATSAFL DNPHPVGVNY VDEGSRQFVA VAELLASKLI DSSRESDESN SDVPFVQAYS KFADDNPRHL RVKTGGKMAN ALTNVIRSY YSINAPAIVP QVEIDRLASK ATVSGDMYNS YAIFNSVPIV EVLSPARTTV SIVGSDRADV TMLNTGAGAA N ITFNFGQI AETVILKGSV PFQLARLNQP MPAARFTYKL RPLDGPFIVV LPVGNPLVIS ATAATRIQVP LAFNKALVES GF QTAMNDG LFDIQNVNYY SSFDEFIISQ YHAQDGINRV STCVILGLAL QAYDQMRRAL PVRRV UniProtKB: VP8 |
-Macromolecule #3: VP10
Macromolecule | Name: VP10 / type: protein_or_peptide / ID: 3 / Details: OR004527 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Banna virus |
Molecular weight | Theoretical: 28.65577 KDa |
Sequence | String: MDVLSKGSLK ELLAHLEKTP LEEAISYRIG TVPYQNVLIS RNEYYNQLYP DTTSLIDGVS REGQRNVNGL IMSIISYVVS GSGHYIPNI GFMLLRRSIL DILTKHDTGL VTNNLNYGII ARNLTVSKMN CEQRKRMLIC FKLLAYKDGN QNDYEIYLNQ N IPLKQIAP ...String: MDVLSKGSLK ELLAHLEKTP LEEAISYRIG TVPYQNVLIS RNEYYNQLYP DTTSLIDGVS REGQRNVNGL IMSIISYVVS GSGHYIPNI GFMLLRRSIL DILTKHDTGL VTNNLNYGII ARNLTVSKMN CEQRKRMLIC FKLLAYKDGN QNDYEIYLNQ N IPLKQIAP NFIPGDMRTV IHNQDQLAIV GIPAYRLTQS TELSIRDDNA KSYKLGYVDW YNSNSFLRER SEFNLIRLKD RD TKYGKLN GW UniProtKB: VP10 |
-Macromolecule #4: VP4
Macromolecule | Name: VP4 / type: protein_or_peptide / ID: 4 / Details: OR004521 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Banna virus |
Molecular weight | Theoretical: 69.7675 KDa |
Sequence | String: MAWVTQAYSS GLSQNSIISL TGNDRTVADG TFNSMIMPRA VIANEREHFM KTRIDKIEHD LNRSAKQEMM DRQSLAEDYN ALNLAVGQE IKLDIATQHQ LNRLGSAMYK ADHERETELT DLINRIRENE VTVNGILENQ KAITAAERAD LLLEVVASTA K SVSAAGRA ...String: MAWVTQAYSS GLSQNSIISL TGNDRTVADG TFNSMIMPRA VIANEREHFM KTRIDKIEHD LNRSAKQEMM DRQSLAEDYN ALNLAVGQE IKLDIATQHQ LNRLGSAMYK ADHERETELT DLINRIRENE VTVNGILENQ KAITAAERAD LLLEVVASTA K SVSAAGRA AADGSGVVPV FGPSVANGIK VGIDIADSVA EAAIAVKESG IITQLNDVYH AFQSVHVAPN DVIKPAAVVA GT STELIGN LQAIYSRLRS HSDIGFKKAT VGDVIPNSYM IKPVNSTEYA SWQLYVIHPV QGSLGLVVQL MGDALTYNVF AQY GNTSAS EFGKTVLTGG ATNTALEGTK VKFQTKVTAQ QALALTMALK DAASMLSQGE LIGYFEQYIN LALEPDNLSL QDNM HKYHH LLTSQNSPID WNYHDEEMHK WLDSRKTTNY DAMQKKDGTV IADIHIPKVF NDLRNTTLHC KLEGKQTIAG YTVYE YLIG PWAHYGDIDY SVVVDTLNEE TKWYCEVIGI DGHLLIEKSV QHKPEKILEL TVNDSGVTSF NGRNHDRLKL KVYVKD SLS VKVFRNWIGI NAPRVKTKMF NDHIGVKYDY SHFDKNISPA HLTLTDLGWH TWDQYNAGNW TNIKP UniProtKB: VP4 |
-Macromolecule #5: VP9
Macromolecule | Name: VP9 / type: protein_or_peptide / ID: 5 / Details: OR004526 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Banna virus |
Molecular weight | Theoretical: 30.581178 KDa |
Sequence | String: MLSETELRAL KKLSTTTSRV VGDSTLALPS NVKLSKGEVE KIAVTKKEMF DELAQCNLPT IELITREHTF NGDVIRFAAW LFLMNGQKL MIANNVAVRM GMQYATNLAG NNVKITYVTS NNVVKLGHIA AGVLANPYSN KGSGLFITYE YNLISNLIET G KVCVLFIT ...String: MLSETELRAL KKLSTTTSRV VGDSTLALPS NVKLSKGEVE KIAVTKKEMF DELAQCNLPT IELITREHTF NGDVIRFAAW LFLMNGQKL MIANNVAVRM GMQYATNLAG NNVKITYVTS NNVVKLGHIA AGVLANPYSN KGSGLFITYE YNLISNLIET G KVCVLFIT SLSTTASSTN SFAYSTCSVP IENWDFNMIK LTAETSCASL TAMTNLVNSL VPGERTRPVG LYVDIPGVTV TT SASSGSL PLTTIPAVTP LIFSAYTKQV EEVGVINTLY ALSYLP UniProtKB: VP9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 293354 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |