+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22931 | |||||||||
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Title | The capsid of Myoviridae Phage XM1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Myoviridae / Vibrio phage / Capsid / HK97 fold / VIRUS | |||||||||
Biological species | Vibrio phage XM1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wang Z / Klose T | |||||||||
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_22931.map.gz | 1.5 GB | EMDB map data format | |
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Header (meta data) | emd-22931-v30.xml emd-22931.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22931_fsc.xml | 33.9 KB | Display | FSC data file |
Images | emd_22931.png | 166.1 KB | ||
Filedesc metadata | emd-22931.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22931 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22931 | HTTPS FTP |
-Validation report
Summary document | emd_22931_validation.pdf.gz | 773.5 KB | Display | EMDB validaton report |
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Full document | emd_22931_full_validation.pdf.gz | 773 KB | Display | |
Data in XML | emd_22931_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | emd_22931_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22931 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22931 | HTTPS FTP |
-Related structure data
Related structure data | 7kmxMC 7kh1C 7kjkC 7klnC 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_22931.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Minor capsid protein
Macromolecule | Name: Minor capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 16.823863 KDa |
Sequence | String: MAFNNAVLQE VSDLPAGEVI KASPHNVSAF EVFQNGLIEG RFVKFDAGSI DILDASATPT IAGIAKRKVT GEIGPGVYST SGIEIDQVA EVINFGFATV TVQDAAAPSK YDPVYAINLD SAEAGKATEN SGATGALAVA DCVFWEQKAA NVWLVRMNKF L |
-Macromolecule #2: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage XM1 (virus) |
Molecular weight | Theoretical: 35.512773 KDa |
Sequence | String: MKKDLKFIKS VYDLKSFSDK AAFAKKTFKD EGGIILARNL EHVSSEIFTQ EFAGLTFLQG GIVVNNEGGY ATSVTKLKLK AEGGFRESG NDTNTTGKIT LSGESDSIPV FTLEGESDWS EIELKQAELQ NVNLPSRYFE AHAELYNRKI DELGYLGQTR T DGTQKTLG ...String: MKKDLKFIKS VYDLKSFSDK AAFAKKTFKD EGGIILARNL EHVSSEIFTQ EFAGLTFLQG GIVVNNEGGY ATSVTKLKLK AEGGFRESG NDTNTTGKIT LSGESDSIPV FTLEGESDWS EIELKQAELQ NVNLPSRYFE AHAELYNRKI DELGYLGQTR T DGTQKTLG LLNYGFVASG AGDTAANLSG DNLYQAIADL ITDQWAGVFN VETYKADRVV MPDTVYNICA KKILNSNGSE MS VLRALMT NFPTVTFGLT TKARDVGGTS RTTAYSSNRR AMQMRIPTPL NVSSVDQRGF KYYVESYFGV AGLDVIEDTA GRH LTGL |
-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 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
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: 30.0 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-7kmx: |