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- EMDB-37378: Structure of full Banna virus -

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Basic information

Entry
Database: EMDB / ID: EMD-37378
TitleStructure of full Banna virus
Map data
Sample
  • Virus: Banna virus
    • Protein or peptide: VP2
    • Protein or peptide: VP8
    • Protein or peptide: VP10VP9
    • Protein or peptide: VP4
    • Protein or peptide: VP9
Keywordsreovirus / complex / capsid protein / VIRUS
Function / homology
Function and homology information


identical protein binding
Similarity search - Function
Seadornavirus VP4 protein / Outer capsid protein VP9/VP10/VP11 / Outer capsid protein VP9, N-terminal / Reoviridae VP9 / Structural protein Vp10, Seadornavirus / Seadornavirus VP8 protein / Seadornavirus Vp10 / Seadornavirus VP2 protein
Similarity search - Domain/homology
VP10 / VP4 / Vp2 / VP9 / VP8
Similarity search - Component
Biological speciesBanna virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi Z / Cao S
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0490000 China
CitationJournal: 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
DepositionSep 5, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37378.png

Downloads & links

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Map

FileDownload / File: emd_37378.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.85 Å
Density
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.03188457 - 0.12424932
Average (Standard dev.)0.0044447156 (±0.011933475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 1140.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37378_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37378_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Banna virus

EntireName: Banna virus
Components
  • Virus: Banna virus
    • Protein or peptide: VP2
    • Protein or peptide: VP8
    • Protein or peptide: VP10VP9
    • Protein or peptide: VP4
    • Protein or peptide: VP9

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Supramolecule #1: Banna virus

SupramoleculeName: 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

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Details: OR004519 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 108.031008 KDa
SequenceString: 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

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Macromolecule #2: VP8

MacromoleculeName: VP8 / type: protein_or_peptide / ID: 2 / Details: OR004525 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 32.786176 KDa
SequenceString: 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 PVRR

UniProtKB: VP8

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Macromolecule #3: VP10

MacromoleculeName: VP10 / type: protein_or_peptide / ID: 3 / Details: OR004527 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 28.65577 KDa
SequenceString: 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

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Details: OR004521 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 69.7675 KDa
SequenceString: 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

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Macromolecule #5: VP9

MacromoleculeName: VP9 / type: protein_or_peptide / ID: 5 / Details: OR004526 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 30.581178 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 34342

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