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- EMDB-75185: Rhesus rotavirus (consensus structure at 4.7 Angstrom resolution ... -

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Basic information

Entry
Database: EMDB / ID: EMD-75185
TitleRhesus rotavirus (consensus structure at 4.7 Angstrom resolution from cryo-ET)
Map dataM reconstruction filtered and sharpened
Sample
  • Virus: Simian rotavirus A strain RRV
    • Protein or peptide: Outer capsid glycoprotein VP7
    • 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 / virus / viral entry / tomography
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / receptor-mediated virion attachment to host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / metal ion binding
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 / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Intermediate capsid protein VP6 / Inner capsid protein VP2 / Outer capsid glycoprotein VP7
Similarity search - Component
Biological speciesSimian rotavirus A strain RRV
Methodsubtomogram averaging / cryo EM / Resolution: 4.7 Å
Authorsde Sautu M / Leistner C / Kirchhausen T / Jenni S / Harrison SC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA13202 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM139386 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI163019 United States
CitationJournal: bioRxiv / Year: 2026
Title: Mechanism of membrane perforation in rotavirus cell entry.
Authors: Marilina de Sautu / Conny Leistner / Tomas Kirchhausen / Simon Jenni / Stephen C Harrison
Abstract: Infectious cell entry by non-enveloped viruses requires delivery of the viral genome -- in many cases enclosed within a large, subviral particle -- across the membrane of an intracellular compartment. ...Infectious cell entry by non-enveloped viruses requires delivery of the viral genome -- in many cases enclosed within a large, subviral particle -- across the membrane of an intracellular compartment. Rotaviruses and other double-strand RNA (dsRNA) viruses introduce into their target cells an inner capsid particle, roughly 700 Å in diameter, that does not uncoat further but instead extrudes capped viral mRNA by virtue of RNA-dependent RNA polymerase and capping activities within it. The delivery agent is an outer protein layer of the virion. We describe here use of cryogenic electron tomography (cryo-ET) to visualize the full course of rhesus rotavirus (RRV) entry, from cell attachment and inward budding of the virion to arrival of the subviral particle in the cytosol. The cryo-tomograms and subtomogram averaging of classified subparticles have enabled us to link high-resolution structures of the virion and its components with time series from live-cell fluorescence microscopy and thus to outline the molecular mechanism of each step in the entry process, including the hitherto elusive membrane perforation step needed for transfer of the subviral particle into the cytosol.
History
DepositionJan 21, 2026-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75185.png

Downloads & links

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Map

FileDownload / File: emd_75185.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationM reconstruction filtered and sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.32 Å/pix.
x 512 pix.
= 1187.84 Å		2.32 Å/pix.
x 512 pix.
= 1187.84 Å		2.32 Å/pix.
x 512 pix.
= 1187.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.020480584 - 0.035660803
Average (Standard dev.)0.000068879555 (±0.0024141204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1187.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75185_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: M reconstruction half map 1

Fileemd_75185_half_map_1.map
AnnotationM reconstruction half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: M reconstruction half map 2

Fileemd_75185_half_map_2.map
AnnotationM reconstruction half map 2
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: 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-#3 / 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: 13 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 37.136531 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
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: Inner capsid protein VP2

MacromoleculeName: Inner capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 103.425992 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
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 #3: Intermediate capsid protein VP6

MacromoleculeName: Intermediate capsid protein VP6 / type: protein_or_peptide / ID: 3 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Simian rotavirus A strain RRV
Molecular weightTheoretical: 44.962773 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet monkey)
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 #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 13 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 52 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 18 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 8565
ExtractionNumber tomograms: 537 / Number images used: 8565 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsPDB-ID 9C1G placed without refinement. Position given by I2 point group symmetry.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-10ic:
Rhesus rotavirus (consensus structure at 4.7 Angstrom resolution from cryo-ET)

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