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- EMDB-45119: Rhesus rotavirus (upright structure at 2.88 Angstrom resolution) -

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Basic information

Entry
Database: EMDB / ID: EMD-45119
TitleRhesus rotavirus (upright structure at 2.88 Angstrom resolution)
Map data
Sample
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Outer capsid glycoprotein VP7
    • Protein or peptide: Outer capsid protein VP4
    • Protein or peptide: Inner capsid protein VP2
    • Protein or peptide: Intermediate capsid protein VP6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION
KeywordsRotavirus / non-enveloped virus / viral particle / VIRAL PROTEIN
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / host cell rough endoplasmic reticulum / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral inner capsid / host cytoskeleton / viral outer capsid / viral nucleocapsid ...viral intermediate capsid / host cell endoplasmic reticulum lumen / host cell rough endoplasmic reticulum / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / permeabilization of host organelle membrane involved in viral entry into host cell / viral inner capsid / host cytoskeleton / viral outer capsid / viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / RNA binding / metal ion binding / membrane
Similarity search - Function
Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain ...Rotavirus VP2 / Rotavirus VP2 protein / Rotavirus A/C, major capsid protein VP6 / Rotavirus major capsid protein VP6 / Glycoprotein VP7 / Glycoprotein VP7, domain 1 / Glycoprotein VP7, domain 2 / Glycoprotein VP7 / Virus capsid protein, alpha-helical / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Viral capsid/haemagglutinin protein / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / Outer capsid protein VP4 / Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesSimian rotavirus A strain RRV
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 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_45119.png

Downloads & links

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Map

FileDownload / File: emd_45119.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-0.04197235 - 0.07544683
Average (Standard dev.)0.0003051154 (±0.003612396)
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_45119_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_45119_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45119_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45119_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 : Simian rotavirus A strain RRV

EntireName: Simian rotavirus A strain RRV
Components
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Outer capsid glycoprotein VP7
    • Protein or peptide: Outer capsid protein VP4
    • Protein or peptide: Inner capsid protein VP2
    • Protein or peptide: Intermediate capsid protein VP6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION

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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: #1-#4 / 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: Outer capsid glycoprotein VP7

MacromoleculeName: Outer capsid glycoprotein VP7 / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 37.136531 KDa
Recombinant expressionOrganism: Simian rotavirus A strain RRV
SequenceString: MYGIEYTTVL TFLISLILLN YILKSLTRMM DFIIYRFLFI VVILSPLLKA QNYGINLPIT GSMDTAYANS TQEETFLTST LCLYYPTEA ATEINDNSWK DTLSQLFLTK GWPTGSVYFK EYTDIASFSV DPQLYCDYNV VLMKYDATLQ LDMSELADLI L NEWLCNPM ...String:
MYGIEYTTVL TFLISLILLN YILKSLTRMM DFIIYRFLFI VVILSPLLKA QNYGINLPIT GSMDTAYANS TQEETFLTST LCLYYPTEA ATEINDNSWK DTLSQLFLTK GWPTGSVYFK EYTDIASFSV DPQLYCDYNV VLMKYDATLQ LDMSELADLI L NEWLCNPM DITLYYYQQT DEANKWISMG SSCTIKVCPL NTQTLGIGCL TTDTATFEEV ATAEKLVITD VVDGVNHKLD VT TATCTIR NCKKLGPREN VAVIQVGGSD VLDITADPTT APQTERMMRI NWKKWWQVFY TVVDYVNQII QAMSKRSRSL NSA AFYYRI

UniProtKB: Outer capsid glycoprotein VP7

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Macromolecule #2: Outer capsid protein VP4

MacromoleculeName: Outer capsid protein VP4 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 86.655586 KDa
Recombinant expressionOrganism: Simian rotavirus A strain RRV
SequenceString: MASLIYRQLL TNSYTVDLSD EIQEIGSTKT QNVTINLGPF AQTGYAPVNW GPGETNDSTT VEPVLDGPYQ PTTFNPPVDY WMLLAPTAA GVVVEGTNNT DRWLATILVE PNVTSETRSY TLFGTQEQIT IANASQTQWK FIDVVKTTQN GSYSQYGPLQ S TPKLYAVM ...String:
MASLIYRQLL TNSYTVDLSD EIQEIGSTKT QNVTINLGPF AQTGYAPVNW GPGETNDSTT VEPVLDGPYQ PTTFNPPVDY WMLLAPTAA GVVVEGTNNT DRWLATILVE PNVTSETRSY TLFGTQEQIT IANASQTQWK FIDVVKTTQN GSYSQYGPLQ S TPKLYAVM KHNGKIYTYN GETPNVTTKY YSTTNYDSVN MTAFCDFYII PREEESTCTE YINNGLPPIQ NTRNIVPLAL SA RNIISHR AQANEDIVVS KTSLWKEMQY NRDITIRFKF ASSIVKSGGL GYKWSEISFK PANYQYTYTR DGEEVTAHTT CSV NGMNDF NFNGGSLPTD FVISRYEVIK ENSYVYVDYW DDSQAFRNMV YVRSLAANLN SVICTGGDYS FALPVGQWPV MTGG AVSLH SAGVTLSTQF TDFVSLNSLR FRFRLTVEEP SFSITRTRVS RLYGLPAANP NNGKEYYEVA GRFSLISLVP SNDDY QTPI TNSVTVRQDL ERQLGELREE FNALSQEIAM SQLIDLALLP LDMFSMFSGI KSTIDAAKSM ATSVMKKFKK SGLANS VST LTDSLSDAAS SISRGASIRS VGSSASAWTD VSTQITDVSS SVSSISTQTS TISRRLRLKE MATQTEGMNF DDISAAV LK TKIDRSTQIS PNTLPDIVTE ASEKFIPNRA YRVINNDEVF EAGTDGRFFA YRVETFDEIP FDVQKFADLV TDSPVISA I IDFKTLKNLN DNYGISRQQA FNLLRSDPRV LREFINQDNP IIRNRIEQLI MQCRL

UniProtKB: Outer capsid protein VP4

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Macromolecule #3: Inner capsid protein VP2

MacromoleculeName: Inner capsid protein VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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 #4: Intermediate capsid protein VP6

MacromoleculeName: Intermediate capsid protein VP6 / type: protein_or_peptide / ID: 4 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 44.962773 KDa
Recombinant expressionOrganism: Simian rotavirus A strain RRV
SequenceString: (FME)DVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN FDFGLLGTTL LNLDAN YVE TARNTIDYFV DFVDNVCMDE MVRESQRNGI APQSDSLRKL SGIKFKRINF DNSSEYIENW NLQNRRQRTG FTFHKPN IF PYSASFTLNR ...String:
(FME)DVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN FDFGLLGTTL LNLDAN YVE TARNTIDYFV DFVDNVCMDE MVRESQRNGI APQSDSLRKL SGIKFKRINF DNSSEYIENW NLQNRRQRTG FTFHKPN IF PYSASFTLNR SQPAHDNLMG TMWLNAGSEI QVAGFDYSCA INAPANIQQF EHIVQLRRVL TTATITLLPD AERFSFPR V INSADGATTW YFNPVILRPN NVEVEFLLNG QIINTYQARF GTIIARNFDT IRLSFQLMRP PNMTPAVAAL FPNAQPFEH HATVGLTLRI ESAVCESVLA DASKTMLANV TSVRQEYAIP VGPVFPPGMN WTDLITNYSP SREDNLQRVF TVASIRSMLV K

UniProtKB: Intermediate capsid protein VP6

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 17 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 76 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 26 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 9 / Number of copies: 7 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 542965
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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