+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16955 | |||||||||
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Title | SA11 Rotavirus Trypsinized Triple Layered Particle | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Rotavirus / 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 | |||||||||
Biological species | Rotavirus / Rotavirus A | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Asensio-Cob D / Perez-Mata C / Gomez-Blanco J / Vargas J / Rodriguez JM / Luque D | |||||||||
Funding support | Spain, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16955.map.gz | 1.2 GB | EMDB map data format | |
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Header (meta data) | emd-16955-v30.xml emd-16955.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16955_fsc.xml | 36.1 KB | Display | FSC data file |
Images | emd_16955.png | 216.5 KB | ||
Filedesc metadata | emd-16955.cif.gz | 7 KB | ||
Others | emd_16955_half_map_1.map.gz emd_16955_half_map_2.map.gz | 1.3 GB 1.3 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16955 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16955 | HTTPS FTP |
-Validation report
Summary document | emd_16955_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_16955_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_16955_validation.xml.gz | 35 KB | Display | |
Data in CIF | emd_16955_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16955 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16955 | HTTPS FTP |
-Related structure data
Related structure data | 8olcMC 8olbC 8oleC 8qtzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16955.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.43 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_16955_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16955_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rotavirus A
Entire | Name: Rotavirus A |
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Components |
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-Supramolecule #1: Rotavirus A
Supramolecule | Name: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Rotavirus SA11 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 |
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Host (natural) | Organism: Chlorocebus aethiops (grivet) |
Molecular weight | Theoretical: 92 MDa |
Virus shell | Shell ID: 1 / Name: TLP / Diameter: 1000.0 Å |
-Macromolecule #1: Outer capsid glycoprotein VP7
Macromolecule | Name: Outer capsid glycoprotein VP7 / type: protein_or_peptide / ID: 1 / Details: Outer capsid glycoprotein VP7 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Rotavirus |
Molecular weight | Theoretical: 37.222602 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: 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 |
-Macromolecule #2: Intermediate capsid protein VP6
Macromolecule | Name: Intermediate capsid protein VP6 / type: protein_or_peptide / ID: 2 / Details: Intermediate capsid protein VP6 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Rotavirus |
Molecular weight | Theoretical: 44.910738 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: 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 |
-Macromolecule #3: Inner capsid protein VP2
Macromolecule | Name: Inner capsid protein VP2 / type: protein_or_peptide / ID: 3 / Details: Inner core protein / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rotavirus |
Molecular weight | Theoretical: 102.853406 KDa |
Recombinant expression | Organism: Chlorocebus aethiops (grivet) |
Sequence | String: 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 |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 26 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 5 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: 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. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 2368 / Average electron dose: 39.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 58000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |