+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60199 | ||||||||||||
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Title | portal-tail of Vibrio cholerae typing phage release VP1 | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | phage / virus / vibrio cholera phage / VIRAL PROTEIN | ||||||||||||
Biological species | Vibrio cholerae (bacteria) / Vibrio cholerae phage (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | ||||||||||||
Authors | Liu HR / Pang H | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: to be published Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states Authors: Liu HR / Pang H | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60199.map.gz | 226 MB | EMDB map data format | |
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Header (meta data) | emd-60199-v30.xml emd-60199.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_60199.png | 65.9 KB | ||
Filedesc metadata | emd-60199.cif.gz | 6 KB | ||
Others | emd_60199_half_map_1.map.gz emd_60199_half_map_2.map.gz | 226 MB 226 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60199 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60199 | HTTPS FTP |
-Validation report
Summary document | emd_60199_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_60199_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_60199_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_60199_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60199 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60199 | HTTPS FTP |
-Related structure data
Related structure data | 8zkmMC 8zkkC 9in6C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_60199.map.gz / Format: CCP4 / Size: 244.1 MB / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60199_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60199_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vibrio cholerae phage
Entire | Name: Vibrio cholerae phage (bacteria) |
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Components |
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-Supramolecule #1: Vibrio cholerae phage
Supramolecule | Name: Vibrio cholerae phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 666 / Sci species name: Vibrio cholerae phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Vibrio cholerae (bacteria) |
-Macromolecule #1: ring protein of release VP1
Macromolecule | Name: ring protein of release VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 26.311119 KDa |
Sequence | String: MSSWDRFDTP WDSIIDESTW EHYTFKYDAS FEAFSSMEVD EDLTITVSVL FASTSDNTVT VGQVLGLTMD NRAGSYFGAG SSWTSEAAV NNEAGSGFQS SHALQLSYSV EDGVISSFGS EAFCSFYNTV SFESSSDVQA AVNSLYNLDV LFSSGSGDSE Q HYVVFGET ...String: MSSWDRFDTP WDSIIDESTW EHYTFKYDAS FEAFSSMEVD EDLTITVSVL FASTSDNTVT VGQVLGLTMD NRAGSYFGAG SSWTSEAAV NNEAGSGFQS SHALQLSYSV EDGVISSFGS EAFCSFYNTV SFESSSDVQA AVNSLYNLDV LFSSGSGDSE Q HYVVFGET ASFESLAEHE TSSQYITHVE CMFNSVVEFE VKTYDWGRPV KPVGSDWSTD TPVVGVWVNE IYNGNKDWGE S |
-Macromolecule #2: adaptor of release VP1
Macromolecule | Name: adaptor of release VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 23.59285 KDa |
Sequence | String: MDKATLVKTI AYRMGNVKGQ DTAIDFELAL SIERLEGQEF VPWFLLSENN FFEGTAQENR IPVPRGFIRE YEEGSLYLRR VAGTGKCLI KKSQDQLLKY EGMTGEPSHY SLTNQYFRIY PVPQEDFKVE LLFYRKSSTL NVEDNPWYEY AAELLVAETI W AMLSARRD ...String: MDKATLVKTI AYRMGNVKGQ DTAIDFELAL SIERLEGQEF VPWFLLSENN FFEGTAQENR IPVPRGFIRE YEEGSLYLRR VAGTGKCLI KKSQDQLLKY EGMTGEPSHY SLTNQYFRIY PVPQEDFKVE LLFYRKSSTL NVEDNPWYEY AAELLVAETI W AMLSARRD KMADYWKSVA ADQMRRLTIL DAERRLANQE IFMG |
-Macromolecule #3: nozzle of release VP1
Macromolecule | Name: nozzle of release VP1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 58.925699 KDa |
Sequence | String: MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA AAAARWNAVN FNGVLLMNNE LDSPQYLAAS GKLEDFPNLP SNVRFRTVAV YKNFILGLGV N FGSGFLDD ...String: MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA AAAARWNAVN FNGVLLMNNE LDSPQYLAAS GKLEDFPNLP SNVRFRTVAV YKNFILGLGV N FGSGFLDD EIYWSHQADP GTMPPNWDYA NAASDSGRTP LPSEGYCVTS EELGSMNIVY KSDSIWTMQL IGGQWIFRFE NK FPGQGIL NKKSVVSFEG KHFVVTQKDI IVHDGYQVRS VADKRVRNFF FTDMNSDYFE RVFVVKDPRV AEVYVFYPSK NSV DGLCDR ALVWNWRDDV WSLLNLRPLK HAAYGYEITG VSITWDNFVG GWESTGLWQA DEDVAKYAPV LHYSFRDVPK LLAP TPQAL FIDEEIEAVW EREDIVIGSI SRDGVPYQDY ERNKSVSSIS FDVDTTEPFD VYIGYKGSLE DSVEWEFAGT VNPME DKRL FCLLTAGLFS MRIISKAQTF ILRSYKITYE FAGEMWA |
-Macromolecule #4: portal of release VP1
Macromolecule | Name: portal of release VP1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 66.026672 KDa |
Sequence | String: MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEVKKTRV ...String: MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEVKKTRV VKGYEGCKTF NVMVYDFIPD PRVALCKYQE GEFFGRRLDL NVLDLKKGAK FGKYFNVEHA EALVAASKEE MY RRDPSIG QQRSLKDSTM TPKGKQVGDI SCVEIFVRLV PKDWGLGDSE FPEMWVFTVA DKKYIVAAEP VNTLDDKFPF HIL ECEIDG YMNKSRGLLE ISAPMNDILT WLFDSHMYNK RQIMNNQFIG DPSALVVKDV ESKEPGKFIR LRPIISQLPV TDVT AQNIQ DVQVVERNMQ RIVGVNDDVA GQSSPSSRRS ATEFRGTTSF ASSRLANLAY FFSVTGFRSL AKSLIVKTQQ LYTVE MKVK VAGDNIKGAQ SIIVKPEDIS GQFDIMPVDG TLPVDRMAQA QFWMQIMSMV AGNPVLGAEY RLGDIFSYTA RLAGLK GID KMKIRILDDD QILALILA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 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: 2.2 µm / Nominal defocus min: 1.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |