+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22917 | |||||||||
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Title | Myoviridae Phage XM1 Neck Region (12-fold) | |||||||||
Map data | 12 fold average for phage XM1 neck | |||||||||
Sample |
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Biological species | Vibrio phage XM1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang Z / Klose T / Jiang W / Kuhn RJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Biorxiv / Year: 2021 Title: Structure of Vibrio phage XM1, a simple contractile DNA injection machine Authors: Wang Z / Fokine A / Guo X / Jiang W / Rossmann MG / Kuhn RJ / Luo ZH / Klose T | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22917.map.gz | 38.8 MB | EMDB map data format | |
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Header (meta data) | emd-22917-v30.xml emd-22917.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22917_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_22917.png | 203.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22917 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22917 | HTTPS FTP |
-Validation report
Summary document | emd_22917_validation.pdf.gz | 395.9 KB | Display | EMDB validaton report |
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Full document | emd_22917_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | emd_22917_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | emd_22917_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22917 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22917 | HTTPS FTP |
-Related structure data
Related structure data | 7klnMC 7kh1C 7kjkC 7kmxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22917.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 12 fold average for phage XM1 neck | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Vibrio phage XM1
Entire | Name: Vibrio phage XM1 (virus) |
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Components |
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-Supramolecule #1: Vibrio phage XM1
Supramolecule | Name: Vibrio phage XM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2748688 / Sci species name: Vibrio phage XM1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Vibrio rotiferianus (bacteria) |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 47.018758 KDa |
Sequence | String: MKFFDGVKDV LSGLINRRNS MARNRVSHRY LSDEEMRVMY KAGLMSKIIR LKAGYALNDT LKFESTQDQE IYKKRLSKHV KNATKFMLG FGRGVIVVFK NGDDLSKPLE RGVDPKLLKI RVFSGDIAKG NNPDNDLRSE RYYKPKNYTI KGHTIHWTRV V DFTYYMPS ...String: MKFFDGVKDV LSGLINRRNS MARNRVSHRY LSDEEMRVMY KAGLMSKIIR LKAGYALNDT LKFESTQDQE IYKKRLSKHV KNATKFMLG FGRGVIVVFK NGDDLSKPLE RGVDPKLLKI RVFSGDIAKG NNPDNDLRSE RYYKPKNYTI KGHTIHWTRV V DFTYYMPS ENELPDYYYG GMSESELIYE QFINDSVVQR ASGSIIEKAS TFVYKIKGYK QLIQAKKEED IIKYVSTCED GR SIYGGLI TDADDEVSTL TQSLTDLDKV DNVTLRRIAM VTGLGMTVLI GEQASGLNAS GEKERQGFQD TIENLQSDYL EDP LNRLAE IFQLGFIEFK DNQGQSANER VEYDKKAVDV AKVLWELGED YGAYLKDKDV VQADDWDNFW KEKDENSEVD ESLP LGDLF SSGDVNG |
-Macromolecule #2: Head completion protein, gp1
Macromolecule | Name: Head completion protein, gp1 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 12.746998 KDa |
Sequence | String: MALIDDFKAR FPNLDGSLVD ALVPVYENNY SCYYGGSYEN DCDKEAILLL IAHLVVTDPS YSGDESSSRA VASQSVGSVS VSFVAGSTG SDWTNWLNST RYGQLFLMVT SNNMGPSFA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 50 mM Tris, pH 7.5, 100 mM NaCl, 8 mM MgSO4 |
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Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7kln: |