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Yorodumi- EMDB-46681: Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-46681 | |||||||||||||||||||||||||||
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Title | Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model | |||||||||||||||||||||||||||
Map data | Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model | |||||||||||||||||||||||||||
Sample |
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Keywords | Bacteriophage / Mycobacteriophage Bxb1 / capsid / portal / VIRUS / VIRAL PROTEIN | |||||||||||||||||||||||||||
Function / homology | Portal protein / Phage portal protein, SPP1 Gp6-like / Phage capsid / Phage capsid family / Major capsid protein / Portal protein Function and homology information | |||||||||||||||||||||||||||
Biological species | Mycobacterium phage Bxb1 (virus) | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||||||||
Authors | Freeman KG / White SJ / Huet A / Conway JF | |||||||||||||||||||||||||||
Funding support | United States, Taiwan, 8 items
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Citation | Journal: To Be Published Title: Structure and infection dynamics of mycobacteriophage Bxb1 Authors: Freeman KG / Mondal S / Macale LS / Podgorski J / White SJ / Silva B / Ortiz V / Huet A / Narsico JT / Ho MC / Jacobs-Sera D / Lowary TL / Conway JF / Park D / Hatfull GF | |||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_46681.map.gz | 1 GB | EMDB map data format | |
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Header (meta data) | emd-46681-v30.xml emd-46681.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_46681.png | 121.8 KB | ||
Filedesc metadata | emd-46681.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-46681 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-46681 | HTTPS FTP |
-Validation report
Summary document | emd_46681_validation.pdf.gz | 627.5 KB | Display | EMDB validaton report |
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Full document | emd_46681_full_validation.pdf.gz | 627.1 KB | Display | |
Data in XML | emd_46681_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_46681_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-46681 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-46681 | HTTPS FTP |
-Related structure data
Related structure data | 9d9wMC 9d93C 9d94C 9d9lC 9d9xC C: citing same article (ref.) M: atomic model generated by this map |
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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_46681.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Mycobacteriophage Bxb1 C1 Capsid and Portal - Composite map and model | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2366 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Mycobacterium phage Bxb1
Entire | Name: Mycobacterium phage Bxb1 (virus) |
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Components |
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-Supramolecule #1: Mycobacterium phage Bxb1
Supramolecule | Name: Mycobacterium phage Bxb1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: Portal and connector complex of Bxb1, containing five protein subunit types. This is a composite map, and related entries for consensus and locally refined maps are noted. NCBI-ID: 2902907 / Sci species name: Mycobacterium phage Bxb1 / Sci species strain: Mycobacterium phage Bxb1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium phage Bxb1 (virus) |
Molecular weight | Theoretical: 41.875461 KDa |
Sequence | String: MGFSADHSQI AQTKDTMFTG YLDPVQAKDY FAEAEKTSIV QRVAQKIPMG ATGIVIPHWT GDVSAQWIGE GDMKPITKGN MTKRDVHPA KIATIFVASA ETVRANPANY LGTMRTKVAT AIAMAFDNAA LHGTNAPSAF QGYLDQSNKT QSISPNAYQG L GVSGLTKL ...String: MGFSADHSQI AQTKDTMFTG YLDPVQAKDY FAEAEKTSIV QRVAQKIPMG ATGIVIPHWT GDVSAQWIGE GDMKPITKGN MTKRDVHPA KIATIFVASA ETVRANPANY LGTMRTKVAT AIAMAFDNAA LHGTNAPSAF QGYLDQSNKT QSISPNAYQG L GVSGLTKL VTDGKKWTHT LLDDTVEPVL NGSVDANGRP LFVESTYESL TTPFREGRIL GRPTILSDHV AEGDVVGYAG DF SQIIWGQ VGGLSFDVTD QATLNLGSQE SPNFVSLWQH NLVAVRVEAE YGLLINDVNA FVKLTFDPVL TTYALDLDGA SAG NFTLSL DGKTSANIAY NASTATVKSA IVAIDDGVSA DDVTVTGSAG DYTITVPGTL TADFSGLTDG EGASISVVSV G UniProtKB: Major capsid protein |
-Macromolecule #2: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium phage Bxb1 (virus) |
Molecular weight | Theoretical: 53.822113 KDa |
Sequence | String: MAETESIDPE KLRDQLLDAF ENKQNELKSS KAYYDAERRP DAIGLAVPLD MRKYLAHVGY PRTYVDAIAE RQELEGFRIP SANGEEPES GGENDPASEL WDWWQANNLD IEATLGHTDA LIYGTAYITI SMPDPEVDFD VDPEVPLIRV EPPTALYAEV D PRTRKVLY ...String: MAETESIDPE KLRDQLLDAF ENKQNELKSS KAYYDAERRP DAIGLAVPLD MRKYLAHVGY PRTYVDAIAE RQELEGFRIP SANGEEPES GGENDPASEL WDWWQANNLD IEATLGHTDA LIYGTAYITI SMPDPEVDFD VDPEVPLIRV EPPTALYAEV D PRTRKVLY AIRAIYGADG NEIVSATLYL PDTTMTWLRA EGEWEAPTST PHGLEMVPVI PISNRTRLSD LYGTSEISPE LR SVTDAAA QILMNMQGTA NLMAIPQRLI FGAKPEELGI NAETGQRMFD AYMARILAFE GGEGAHAEQF SAAELRNFVD ALD ALDRKA ASYSGLPPQY LSSSSDNPAS AEAIKAAESR LVKKVERKNK IFGGAWEQAM RLAYKMVKGG DIPTEYYRME TVWR DPSTP TYAAKADAAA KLFANGAGLI PRERGWVDMG YTIVEREQMR QWLEQDQKQG LGLIGSLYGA STPEGKPGEA PVGEP PAPE PDAA UniProtKB: Portal protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Number images used: 33132 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |