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- EMDB-16954: SA11 Rotavirus Non-tripsinized Triple Layered Particle -

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Basic information

Entry
Database: EMDB / ID: EMD-16954
TitleSA11 Rotavirus Non-tripsinized Triple Layered Particle
Map dataReuploaded main map
Sample
  • Virus: Rotavirus A
    • Protein or peptide: Inner capsid protein VP2
    • Protein or peptide: Outer capsid glycoprotein VP7
    • Protein or peptide: Intermediate capsid protein VP6
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsRotavirus / dsRNA virus / VIRUS
Function / homology
Function and homology information


viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope ...viral intermediate capsid / host cell endoplasmic reticulum lumen / T=2 icosahedral viral capsid / T=13 icosahedral viral capsid / viral inner capsid / viral outer capsid / viral nucleocapsid / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / structural molecule activity / RNA binding / membrane / 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
Outer capsid glycoprotein VP7 / Inner capsid protein VP2 / Intermediate capsid protein VP6
Similarity search - Component
Biological speciesRotavirus / Rotavirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsAsensio-Cob D / Perez-Mata C / Gomez-Blanco J / Vargas J / Rodriguez JM / Luque D
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesISCIII-AESI PI20CIII/00014 Spain
CitationJournal: To Be Published
Title: Structural basis of rotavirus spike proteolytic activation
Authors: Asensio-Cob D / Perez-Mata C / Gomez-Blanco J / Vargas J / Rodriguez JM / Luque D
History
DepositionMar 30, 2023-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16954.png

Downloads & links

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Map

FileDownload / File: emd_16954.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReuploaded main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 800 pix.
= 1072. Å		1.34 Å/pix.
x 800 pix.
= 1072. Å		1.34 Å/pix.
x 800 pix.
= 1072. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.010321567 - 0.09428734
Average (Standard dev.)0.0005239769 (±0.0080780145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-399-399-399
Dimensions800800800
Spacing800800800
CellA=B=C: 1072.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16954_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_16954_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 : Rotavirus A

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

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Supramolecule #1: Rotavirus A

SupramoleculeName: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Rotavirus SA11 Non-trypsinized TLP / NCBI-ID: 28875 / Sci species name: Rotavirus A / Sci species strain: SA11 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chlorocebus aethiops (grivet)
Molecular weightTheoretical: 92 MDa
Virus shellShell ID: 1 / Name: TLP / Diameter: 1000.0 Å

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Macromolecule #1: Inner capsid protein VP2

MacromoleculeName: Inner capsid protein VP2 / type: protein_or_peptide / ID: 1 / Details: Inner core protein / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus
Molecular weightTheoretical: 102.853406 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MAYRKRGARR ETNLKQDERM QEKEDSKNIN NDSPKSQLSE KVLSKKEEII TDNQEEVKIS DEVKKSNKEE SKQLLEVLKT KEEHQKEVQ YEILQKTIPT FEPKESILKK LEDIKPEQAK KQTKLFRIFE PKQLPIYRAN GERELRNRWY WKLKRDTLPD G DYDVREYF ...String:
MAYRKRGARR ETNLKQDERM QEKEDSKNIN NDSPKSQLSE KVLSKKEEII TDNQEEVKIS DEVKKSNKEE SKQLLEVLKT KEEHQKEVQ YEILQKTIPT FEPKESILKK LEDIKPEQAK KQTKLFRIFE PKQLPIYRAN GERELRNRWY WKLKRDTLPD G DYDVREYF LNLYDQVLME MPDYLLLKDM AVENKNSRDA GKVVDSETAA ICDAIFQDEE TEGAVRRFIA EMRQRVQADR NV VNYPSIL HPIDHAFNEY FLQHQLVEPL NNDIIFNYIP ERIRNDVNYI LNMDRNLPST ARYIRPNLLQ DRLNLHDNFE SLW DTITTS NYILARSVVP DLKELVSTEA QIQKMSQDLQ LEALTIQSET QFLTGINSQA ANDCFKTLIA AMLSQRTMSL DFVT TNYMS LISGMWLLTV IPNDMFIRES LVACQLAIIN TIVYPAFGMQ RMHYRNGDPQ TPFQIAEQQI QNFQVANWLH FVNYN QFRQ VVIDGVLNQV LNDNIRNGHV VNQLMEALMQ LSRQQFPTMP VDYKRSIQRG ILLLSNRLGQ LVDLTRLLSY NYETLM ACI TMNMQHVQTL TTEKLQLTSV TSLCMLIGNA TVIPSPQTLF HYYNVNVNFH SNYNERINDA VAIITAANRL NLYQKKM KS IVEDFLKRLQ IFDVARVPDD QMYRLRDRLR LLPVEIRRLD IFNLIAMNME QIERASDKIA QGVIIAYRDM QLERDEMY G YVNIARNLDG FQQINLEELM RSGDYAQITN MLLNNQPVAL VGALPFITDS SVISLIAKLD ATVFAQIVKL RKVDTLKPI LYKINSDSND FYLVANYDWI PTSTTKVYKQ VPQQFDFRAS MHMLTSNLTF TVYSDLLAFV SADTVEPINA VAFDNMRIMN EL

UniProtKB: Inner capsid protein VP2

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Macromolecule #2: Outer capsid glycoprotein VP7

MacromoleculeName: Outer capsid glycoprotein VP7 / type: protein_or_peptide / ID: 2 / Details: Outer capsid glycoprotein VP7 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus
Molecular weightTheoretical: 37.222602 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MYGIEYTTVL TFLISIILLN YILKSLTRIM DFIIYRFLFI IVILSPFLRA QNYGINLPIT GSMDTAYANS TQEETFLTST LCLYYPTEA ATEINDNSWK DTLSQLFLTK GWPTGSVYFK EYTNIASFSV DPQLYCDYNV VLMKYDATLQ LDMSELADLI L NEWLCNPM ...String:
MYGIEYTTVL TFLISIILLN YILKSLTRIM DFIIYRFLFI IVILSPFLRA QNYGINLPIT GSMDTAYANS TQEETFLTST LCLYYPTEA ATEINDNSWK DTLSQLFLTK GWPTGSVYFK EYTNIASFSV DPQLYCDYNV VLMKYDATLQ LDMSELADLI L NEWLCNPM DITLYYYQQT DEANKWISMG SSCTIKVCPL NTQTLGIGCL TTDATTFEEV ATAEKLVITD VVDGVNHKLD VT TATCTIR NCKKLGPREN VAVIQVGGSD ILDITADPTT APQTERMMRI NWKKWWQVFY TVVDYVDQII QVMSKRSRSL NSA AFYYRV

UniProtKB: Outer capsid glycoprotein VP7

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Macromolecule #3: Intermediate capsid protein VP6

MacromoleculeName: Intermediate capsid protein VP6 / type: protein_or_peptide / ID: 3 / Details: Intermediate capsid protein VP6 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Rotavirus
Molecular weightTheoretical: 44.910738 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN FNFGLLGTTL LNLDANYVET ARNTIDYFV DFVDNVCMDE MVRESQRNGI APQSDSLRKL SAIKFKRINF DNSSEYIENW NLQNRRQRTG FTFHKPNIFP Y SASFTLNR ...String:
MDVLYSLSKT LKDARDKIVE GTLYSNVSDL IQQFNQMIIT MNGNEFQTGG IGNLPIRNWN FNFGLLGTTL LNLDANYVET ARNTIDYFV DFVDNVCMDE MVRESQRNGI APQSDSLRKL SAIKFKRINF DNSSEYIENW NLQNRRQRTG FTFHKPNIFP Y SASFTLNR SQPAHDNLMG TMWLNAGSEI QVAGFDYSCA INAPANIQQF EHIVPLRRVL TTATITLLPD AERFSFPRVI NS ADGATTW FFNPVILRPN NVEVEFLLNG QIINTYQARF GTIVARNFDT IRLSFQLMRP PNMTPAVAVL FPNAQPFEHH ATV GLTLRI ESAVCESVLA DASETLLANV TSVRQEYAIP VGPVFPPGMN WTDLITNYSP SREDNLQRVF TVASIRSMLI K

UniProtKB: Intermediate capsid protein VP6

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 26 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1465 / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11221
Startup modelType of model: EMDB MAP
EMDB ID:

2574

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 10815
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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