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- EMDB-36871: In situ structure of RNA-dependent RNA polymerase in full BAV par... -

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Basic information

Entry
Database: EMDB / ID: EMD-36871
TitleIn situ structure of RNA-dependent RNA polymerase in full BAV particles
Map data
Sample
  • Virus: Banna virus
    • Protein or peptide: RNA-directed RNA polymerase (Fragment)
    • Protein or peptide: VP2
Keywordsreovirus / RdRp / complex / inner capsid protein / VIRUS
Function / homology
Function and homology information


viral genome replication / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / RNA binding
Similarity search - Function
RNA-directed RNA polymerase / Seadornavirus VP2 protein / Seadornavirus inner capsid protein VP2 / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase / Vp2
Similarity search - Component
Biological speciesBanna virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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
DepositionJul 17, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36871.png

Downloads & links

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Map

FileDownload / File: emd_36871.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 450 pix.
= 427.5 Å		0.95 Å/pix.
x 450 pix.
= 427.5 Å		0.95 Å/pix.
x 450 pix.
= 427.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0019429702 - 1.8514031
Average (Standard dev.)0.021704124 (±0.111544296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 427.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36871_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_36871_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: RNA-directed RNA polymerase (Fragment)
    • Protein or peptide: VP2

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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: RNA-directed RNA polymerase (Fragment)

MacromoleculeName: RNA-directed RNA polymerase (Fragment) / type: protein_or_peptide / ID: 1 / Details: OR004518 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Banna virus
Molecular weightTheoretical: 138.563344 KDa
SequenceString: MDVQEQFEGY LREEVDLLNK FEDSHFKQLE IFYTKSQTDH VINKDKLQFN ALPFHTTLYK EINGKRVRLG TLLNWTKAER LDTIRHESM IKDERLRRLI DFDYGWIDYA VVLQRYLDEG NTIESANILQ FDGDFVNNIK HPTQKNNFLD IKVIKECETY I LMKDDNGI ...String:
MDVQEQFEGY LREEVDLLNK FEDSHFKQLE IFYTKSQTDH VINKDKLQFN ALPFHTTLYK EINGKRVRLG TLLNWTKAER LDTIRHESM IKDERLRRLI DFDYGWIDYA VVLQRYLDEG NTIESANILQ FDGDFVNNIK HPTQKNNFLD IKVIKECETY I LMKDDNGI RDPDILRAWE LNSIPEVIEL DVDGETKKFN LRKEMIKRIQ DEAPVYFFCN PYRYAVANLD PNIPEVRLWL EY FIGSEDF FGFNGPNVIV SKSLLAAKRF EVVVNHLRKV AAFELDVESK EVMNEWIKYI MIDPVYRSYK NRGAFGNLNQ HVF ARTKSE GLSWSLIDIG TTNFELKPTK KVAGSYVNKF NLVDDVLVEE SLKDLRNEGL HKMADVTRRM IDADITPENV KKGK LNRLA LSYCGYTGSH SATAMVKQFN GTKDLDPNCD PMFVDIVKDN MRVYMQEGLQ KYPQGSRKSN RLDILFKGGT SSASS TNEH AVVNGRFRYR SELYRERDVN SSTVFKTATP GQYRVVKKIS AKLKSKNANI VTHPMNFINF KVDDLDIVVN AGSRLV RGT RAKRIITPNY GTIYAASLMT VLPAVRLLSS RASNMGALST QGRIGTTYHG ALPHDVMAPQ LAVTSSDDVS KICVAKD FG QFDTSQWGQI SKAHADGVRS MKAHYSMGHD TLVDLDLNDA SFADLLEVTA MSYERPLKYK MNGLVCESAG VKSGELTT Q TRNTTTNISH STVALDDYNN RAYRLNLPKL ELVTDNKVGD DSVEVLRVVD GSPLTPEIAK LYVNCMQDHA DKNHLEISA KRTIVGNNVA EHIKIWVFKG YLALDVFLDS VTSEKNSFSN LNYLEQVNIL YDMAMTLMIR YCSVQACMTQ FCNDMKLLNG IRAGNYTFI PTPKIICAYG TPEICLRAPE IRSFGRYLPI DEDEYSVLND LVASLSTNKP KMDFVAQMFE QNGNQVHGIW L DHFKRKND VNPDGGGIHI SEGLKRLMPE YCERHLNELV YKTLDDKVIR DYTSDIIITN ICKGKLSKAP KLAFFANFYL SL TGFNGVD SPYLTADEGV KNVHRVIGLS YRNTLSTSPT ANVDRILRNN PGSAPAYLTG NDILGVLSDY PYQNWRTVVE LLD ITEPSA TAIIEVATNQ MHAYLADKDL NTANLFDNTS RTYDISDRTY PKFVNITSNL SNSNRRGFQL EAMKHIIYMA RRGI ATLAN THPSKIGNTV YYDY

UniProtKB: RNA-directed RNA polymerase

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Details: OR004519 / Number of copies: 11 / 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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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 210465
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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