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- EMDB-45123: Rhesus rotavirus (VP1 structure at 2.65 Angstrom resolution) -

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Basic information

Entry
Database: EMDB / ID: EMD-45123
TitleRhesus rotavirus (VP1 structure at 2.65 Angstrom resolution)
Map data
Sample
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Inner capsid protein VP2
    • Protein or peptide: RNA-directed RNA polymerase
KeywordsRotavirus / non-enveloped virus / viral particle / VIRAL PROTEIN
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid / viral genome replication / virion component / viral nucleocapsid / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
Rotavirus VP1 RNA-directed RNA polymerase, C-terminal / Viral RNA-directed RNA polymerase, 4-helical domain / Rotavirus VP1 C-terminal domain / RNA-directed RNA polymerase, luteovirus / Viral RNA-directed RNA-polymerase / Rotavirus VP2 / Rotavirus VP2 protein / RNA-directed RNA polymerase, reovirus / RdRp of Reoviridae dsRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase / Inner capsid protein VP2
Similarity search - Component
Biological speciesSimian rotavirus A strain RRV
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsJenni S / Herrmann T / De Sautu M / Harrison SC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA13202 United States
CitationJournal: To Be Published
Title: Rotavirus structure
Authors: Jenni S / Herrmann T / De Sautu M / Harrison SC
History
DepositionMay 29, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45123.png

Downloads & links

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Map

FileDownload / File: emd_45123.map.gz / Format: CCP4 / Size: 13.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 1536 pix.
= 1267.2 Å		0.83 Å/pix.
x 1536 pix.
= 1267.2 Å		0.83 Å/pix.
x 1536 pix.
= 1267.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.055566445 - 0.09411559
Average (Standard dev.)0.0003238041 (±0.0044066655)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions153615361536
Spacing153615361536
CellA=B=C: 1267.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45123_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_45123_additional_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_45123_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45123_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Simian rotavirus A strain RRV

EntireName: Simian rotavirus A strain RRV
Components
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Inner capsid protein VP2
    • Protein or peptide: RNA-directed RNA polymerase

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Supramolecule #1: Simian rotavirus A strain RRV

SupramoleculeName: Simian rotavirus A strain RRV / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 444185 / Sci species name: Simian rotavirus A strain RRV / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Inner capsid protein VP2

MacromoleculeName: Inner capsid protein VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 103.425992 KDa
Recombinant expressionOrganism: Simian rotavirus A strain RRV
SequenceString: MAYRKRGARR ETNLKQDDRM QEKEENKNVN TNSENKNATK PQLSEKVLSQ KEEVITDNQE EIKIADEVKK SNKEESKQLL EVLKTKEEH QKEVQYEILQ KTIPTFEPKE SILKKLEDIK PEQVKKQTKL FRIFEPRQLP VYRANGEKEL RNRWYWKLKR D TLPDGDYD ...String:
MAYRKRGARR ETNLKQDDRM QEKEENKNVN TNSENKNATK PQLSEKVLSQ KEEVITDNQE EIKIADEVKK SNKEESKQLL EVLKTKEEH QKEVQYEILQ KTIPTFEPKE SILKKLEDIK PEQVKKQTKL FRIFEPRQLP VYRANGEKEL RNRWYWKLKR D TLPDGDYD VREYFLNLYD QVLTEMPDYL LLKDMAVENK NSRDAGKVVD SETAAICDAI FQDEETEGVV RRFIAEMRQR VQ ADRNVVN YPSILHPIDH AFNEYFLQHQ LVEPLNNDII FNYIPERIRN DVNYILNMDR NLPSTARYIR PNLLQDRLNL HDN FESLWD TITTSNYILA RSVVPDLKEL VSTEAQIQKM SQDLQLEALT IQSETQFLTG INSQAANDCF KTLIAAMLSQ RTMS LDFVT TNYMSLISGM WLLTVVPNDM FIRESLVACQ LAIINTIIYP AFGMQRMHYR NGDPQTPFQI AEQQIQNFQV ANWLH FVNN NQFRQVVIDG VLNQVLNDNI RNGHVVNQLM EALMQLSRQQ FPTMPVDYKR SIQRGILLLS NRLGQLVDLT RLLAYN YET LMACITMNMQ HVQTLTTEKL QLTSVTSLCM LIGNATVIPS PQTLFHYYNV NVNFHSNYNE RINDAVAIIT AANRLNL YQ KKMKSIVEDF LKRLQIFDIS RVPDDQMYRL RDRLRLLPVE IRRLDIFNLI LMNMEQIERA SDKIAQGVII AYRDMQLE R DEMYGYVNIA RNLDGFQQIN LEELMRTGDY AQITNMLLNN QPVALVGALP FITDSSVISL VAKLDATVFA QIVKLRKVD TLKPILYKIN SDSNDFYLVA NYDWVPTSTT KVYKQIPQQF DFRASMHMLT SNLTFTVYSD LLAFVSADTV EPINAVAFDN MRIMNEL

UniProtKB: Inner capsid protein VP2

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Macromolecule #2: RNA-directed RNA polymerase

MacromoleculeName: RNA-directed RNA polymerase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed RNA polymerase
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 125.276305 KDa
Recombinant expressionOrganism: Simian rotavirus A strain RRV
SequenceString: MGKYNLILSE YLSFIYNSQS AVQIPIYYSS NSELENRCIE FHSKCLENSK NGLSLKKLFV EYSDVIENAT LLSILSYSYD KYNAVERKL VKYAKGKPLE ADLTVNELDY ENNKITSELF PTAEEYTDLL MDPAILTSLS SNLNAVMFWL EKHENDVAEK L KIYKRRLD ...String:
MGKYNLILSE YLSFIYNSQS AVQIPIYYSS NSELENRCIE FHSKCLENSK NGLSLKKLFV EYSDVIENAT LLSILSYSYD KYNAVERKL VKYAKGKPLE ADLTVNELDY ENNKITSELF PTAEEYTDLL MDPAILTSLS SNLNAVMFWL EKHENDVAEK L KIYKRRLD LFTIVASTVN KYGVPRHNAK YRYEYEVMKD KPYYLVTWAN SSIEMLMSVF SHEDYLIARE LIVLSYSNRS TL AKLVSSP MSILVALVDI NGTFITNEEL ELEFSNKYVR AIVPDQTFDE LKQMLDNMRK AGLTDIPKMI QDWLVDCSIE KFP LMAKIY SWSFHVGFRK QKMLDAALDQ LKTEYTEDVD DEMYREYTML IRDEVVKMLE EPVKHDDHLL QDSELAGLLS MSSA SNGES RQLKFGRKTI FSTKKNMHVM DDMANGRYTP GIIPPVNVDK PIPLGRRDVP GRRTRIIFIL PYEYFIAQHA VVEKM LIYA KHTREYAEFY SQSNQLLSYG DVTRFLSNNS MVLYTDVSQW DSSQHNTQPF RKGIIMGLDM LANMTNDARV IQTLNL YKQ TQINLMDSYV QIPDGNVIKK IQYGAVASGE KQTKAANSIA NLALIKTVLS RISNKYSFAT KIIRVDGDDN YAVLQFN TE VTKQMVQDVS NDVRETYARM NTKVKALVST VGIEIAKRYI AGGKIFFRAG INLLNNEKKG QSTQWDQAAV LYSNYIVN R LRGFETDREF ILTKIMQMTS VAITGSLRLF PSERVLTTNS TFKVFDSEDF IIEYGTTDDE VYIQRAFMSL SSQKSGIAD EIAASSTFKN YVSRLSEQLL FSKNNIVSRG IALTEKAKLN SYAPISLEKR RAQISALLTM LQKPVTFKSS KITINDILRD IKPFFTVNE AHLPIQYQKF MPTLPDNVQY IIQCIGSRTY QIEDDGSKSA ISRLISKYSV YKPSIEELYK VISLHENEIQ L YLISLGIP KIDADTYVGS KIYSQDKYRI LESYVYNLLS INYGCYQLFD FNSPDLEKLI RIPFKGKIPA VTFILHLYAK LE VINHAIK NGSWISLFCN YPKSEMIKLW KKMWNITSLR SPYTNANFFQ D

UniProtKB: RNA-directed RNA polymerase

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 469892
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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