+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60197 | ||||||||||||
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Title | Portal-tail of Vibrio cholerae typing phage mature 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: 3.6 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_60197.map.gz | 225.6 MB | EMDB map data format | |
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Header (meta data) | emd-60197-v30.xml emd-60197.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_60197.png | 71.8 KB | ||
Filedesc metadata | emd-60197.cif.gz | 6.1 KB | ||
Others | emd_60197_half_map_1.map.gz emd_60197_half_map_2.map.gz | 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60197 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60197 | HTTPS FTP |
-Validation report
Summary document | emd_60197_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_60197_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_60197_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_60197_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60197 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60197 | HTTPS FTP |
-Related structure data
Related structure data | 8zkkMC 8zkmC 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_60197.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_60197_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60197_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: No |
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-Macromolecule #1: nozzle gp16
Macromolecule | Name: nozzle gp16 / 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: 59.015762 KDa |
Sequence | String: MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA GSGRRWNAVN FNGVLLMNNE LDSPQYLAAS GKLEDFPNLP SNVRFRTVAV YKNFILGLGV N FGSGFLDD ...String: MEVTHKQFDL SGFLPDQAPD TLKSGAISRG FNVKPTILGW EKSGGFRETN TAPTNEKDFI FFWSPAIGDN RWFSGGDKTV QQVEGNVVS DVSRTGGYTA GSGRRWNAVN 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 FAGEMWS |
-Macromolecule #2: portal gp5
Macromolecule | Name: portal gp5 / 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: 73.263602 KDa |
Sequence | String: MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEEEEEII ...String: MEILYTGASE SLHSTILKAL LERIDLGDTF ISDNYTRWQA TERYYMMYKI PNKKDKAAIE KWNKGDTDFK SLVMPYSYAQ LMTAHAYMV NVFLNRDPIF QTDSLNGDGT ERELALESML QYQVKAGEME PSLLVWFMDA LRYGVGVLGD YWEEHVFHQT V FEEEEEII DGVPTGNMKK VKKTRVVKGY EGCKTFNVMV YDFIPDPRVA LCKYQEGEFF GRRLDLNVLD LKKGAKFGKY FN VEHAEAL VAASKEEMYR RDPSIGQQRS LKDSTMTPKG KQVGDISCVE IFVRLVPKDW GLGDSEFPEM WVFTVADKKY IVA AEPVNT LDDKFPFHIL ECEIDGYMNK SRGLLEISAP MNDILTWLFD SHMYNKRQIM NNQFIGDPSA LVVKDVESKE PGKF IRLRP TAYGRDVRSI ISQLPVTDVT AQNIQDVQVV ERNMQRIVGV NDDVAGQSSP SSRRSATEFR GTTSFASSRL ANLAY FFSV TGFRSLAKSL IVKTQQLYTV EMKVKVAGDN IKGAQSIIVK PEDISGQFDI MPVDGTLPVD RMAQAQFWMQ IMSMVA GNP VLGAEYRLGD IFSYTARLAG LKGIDKMKIR ILDDDQILAL ILAQQKGGAD VQPTGQPTTQ GVGNPTGVNE PAPSVTQ GT PGLSGLQALM |
-Macromolecule #3: adaptor gp12
Macromolecule | Name: adaptor gp12 / type: protein_or_peptide / ID: 3 / 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 #4: ring protein gp10
Macromolecule | Name: ring protein gp10 / type: protein_or_peptide / ID: 4 / 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 #5: gp13
Macromolecule | Name: gp13 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Molecular weight | Theoretical: 10.025203 KDa |
Sequence | String: MALETWDANS TPATLNTAWP EATDPLNKGD DHIRLLKTVV VNFWNKVFDG SKLKTAVVPA AVNSATAGSG FGGFRYQVVN NSDGTKTLR LFTS |
-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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47456 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |