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- EMDB-55928: OmRV Crown Protein Deletion mutant infectious clone -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55928
TitleOmRV Crown Protein Deletion mutant infectious clone
Map dataFull map of OmRV-CrP deletion mutant
Sample
  • Virus: Omono River virus
    • Protein or peptide: Omono River Virus AK4 strain Subunit A
KeywordsOmono River Virus / Artiviruses / dsRNA viruses / Capsid / Infectioius clone / VIRUS
Biological speciesOmono River virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang H / Okamoto K
Funding support Sweden, Norway, 4 items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2023-01857 Sweden
Carl Trygger Foundation23:2703 Sweden
Research Council of Norway324266 Norway
CitationJournal: To Be Published
Title: OmRV Crown protein deletion mutant infectious clone
Authors: Hernandez GG / Wang H / Manesco C / Okamoto K
History
DepositionDec 3, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55928.png

Downloads & links

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Map

FileDownload / File: emd_55928.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map of OmRV-CrP deletion mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 600 pix.
= 571.2 Å		0.95 Å/pix.
x 600 pix.
= 571.2 Å		0.95 Å/pix.
x 600 pix.
= 571.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.952 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7329
Minimum - Maximum-3.099884 - 5.4831557
Average (Standard dev.)0.03675528 (±0.24425115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 571.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of OmRV-CrP deletion mutant

Fileemd_55928_half_map_1.map
AnnotationHalf map A of OmRV-CrP deletion mutant
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of OmRV-CrP deletion mutant

Fileemd_55928_half_map_2.map
AnnotationHalf map B of OmRV-CrP deletion mutant
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Omono River virus

EntireName: Omono River virus
Components
  • Virus: Omono River virus
    • Protein or peptide: Omono River Virus AK4 strain Subunit A

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Supramolecule #1: Omono River virus

SupramoleculeName: Omono River virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Infectious DNA clone / NCBI-ID: 753758 / Sci species name: Omono River virus / Sci species strain: AK4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Omono River Virus AK4 strain Subunit A

MacromoleculeName: Omono River Virus AK4 strain Subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Omono River virus
Molecular weightTheoretical: 183.716047 KDa
Recombinant expressionOrganism: Ades (beetle)
SequenceString: MPGYSANYRE GPVIVPSGDQ VVTSPTSHGR SKGVSSELLT VGGQTYKAIA SNEVVKSGQA KGEQKFFDEN AKIVLLGTFP FKKDLTKEG VEPNPGPVVS DPYANTIYGP LPTHKEAAIN LGEQPSAPVK QRPKRHAVVD RVYKTLTLKN GILVTKVVIA G VATYIVYK ...String:
MPGYSANYRE GPVIVPSGDQ VVTSPTSHGR SKGVSSELLT VGGQTYKAIA SNEVVKSGQA KGEQKFFDEN AKIVLLGTFP FKKDLTKEG VEPNPGPVVS DPYANTIYGP LPTHKEAAIN LGEQPSAPVK QRPKRHAVVD RVYKTLTLKN GILVTKVVIA G VATYIVYK VGSEVWSWYA AITKPLLGVQ TAVKEEYHTL QHKYDYQWYD YFCPMCLLSK YIANSGVNGT DAEHHNHVMH AL NGNIDCD SSVFGNNFNI TTSPQTLTMS GPLAPGKYQT TLTVQALIGG TGVVVGTVTF AGKTVAYQVF DDSFASFDLG TVT VSASTA PSVIWTGSTG ATLTMAVNII CKPITPTSVA ISGQPIWTTP YAPAQAVMTV PAVAKALKNT QRAADLSTRN KTRH GSNNA ISVLNQLATQ IDVEDQRLPI YKIEGEREGT HEPSFSCQLT FRGMTKSAFG KRTKHEAKTA AASLILEELT RKSNS TWPA DAKLTLSGWV RDLTEEGIEP NPGPIANEDG AECWDPEELK MLQAMMAREQ QKVLPKMIDD PKLVLDLDEM QQLAPQ ESC NKTVSVDEYQ EHVRHMSNYS GAVGEAFAVV RWYLLNETTN RFAPLVVMDD SMDEPIATPV DVSPAKRPSG VSRRSDK EE EKPKKPPKKE KIVPAPQPPK TQEQLDEERK FAMQRIADRI KSDPIKLLTW IKRPTSTKFK REVLSLAFDI PHINSKPS L DQYETIVYCY FNDIPDDELT IMLLQYDRKW TSLSTDCKLS ILSACNVRAS LEAAKAHNKL MHAYNGNPIS ADFSEVENA PSFLSLAENT DEVLKPYTGL EIQTIITNIV GDANPNQSRI FDQDRLRGNQ YSAGGLVTQN AVSAIPFTNL IPRTIRVGNI LVNSANRLQ ITETNVSEYY SNPIIATKLS EMISDQVKNN QFSTWRRDNT SLQGFNAFDI ATINTAILPN GLSLESMLLK L SLLHSIKA MNVDAASINR SQYQVIDHNT VPTIGAPAVV GVNNSPVFGE DCGGNNPVYP FGGGTGAIAF HVTLQTVPDE RK SYAIFVP PAILQATSDA NEALALFALS MSEWPHALYT VTKQTTDLAG ANAGQQVFIP TQSTIHIGGR RVLDLIIPRR EIA PNPTTL VAANAMCMVR PQAGPDATAG AIPLAAGQLF NMNFIGAPAF EEWPLTSYLY SWAGRFDITT IRQYMGRLAT MVGV KDAYW AAHELNVALS QVAPKMTTAA GGWAAQAANS AQQSDVCYSS LLTVTRSAAN FPLANQPAAD MRVYDTDPAT WNKVA LGLA TAANLVPEQS MDVPFVVGDA RTSFWERLQA IPMCIAWTMY YHSRGITTLA WDNAYTDNTN KWLQKMVRNT FSTTQS VGT IIPARYGKIV CNLYKNMFHR APAYVATSVG GKELHITHFE RWLPGGTYAN VYSGAGAVVN CFSPVLIPDI WCQYFTA KL PLFAGAFPPA QGQNSTKGFN SKQGLMIHRN QNNNLVAPYL EKFADNSSYF PVGQGPEIND MATWNGRLWM TTGNVQYL D YSGAAIVEAV PPAGELPVGK QIPLLAGENA PIELTNAATT CVPRYSNDGR RIFTYLTTAQ SVIPVQACNR AANLARSCW LLSNVYAEPA LQALGDEVED AFDTLTNSSF LDVAKSVAES AGEVPATKAL TDLQAVDVSS LPSTSDPSNV LSQPAPLMSP PTSSS

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 29.57 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6s2c

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12488
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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