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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Mycobacterium phage Patience | |||||||||
![]() | Sharpened map of ewald sphere corrected postprocess. | |||||||||
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![]() | HK97-fold / T=7 / tailed bacteriophage / VIRUS | |||||||||
Function / homology | Uncharacterized protein / Uncharacterized protein / Capsid protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.39 Å | |||||||||
![]() | Podgorski JM / White SJ | |||||||||
Funding support | 1 items
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![]() | ![]() Title: A novel accessory protein stabilizes the capsid of two actinobacteriophages Authors: Podgorski JM / Porgorski J / Gosselin S / Abad L / Jacobs-Sera D / Brown C / Hatfull G / Gogarten P / Luque A / White SJ | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.7 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.6 KB 22.6 KB | Display Display | ![]() |
Images | ![]() | 312.7 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() ![]() ![]() | 1.8 GB 1.6 GB 1.6 GB 1.6 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 996.4 KB | Display | ![]() |
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Full document | ![]() | 996 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8giuMC ![]() 8sajC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Sharpened map of ewald sphere corrected postprocess. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Ewald sphere corrected map
File | emd_40077_additional_1.map | ||||||||||||
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Annotation | Ewald sphere corrected map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Map after CTF Refinement.
File | emd_40077_additional_2.map | ||||||||||||
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Annotation | Map after CTF Refinement. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of ewald sphere corrected Refine3D After CTFRefine.mrc.
File | emd_40077_half_map_1.map | ||||||||||||
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Annotation | Half map of ewald sphere corrected Refine3D_After_CTFRefine.mrc. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of ewald sphere corrected Refine3D After CTFRefine.mrc.
File | emd_40077_half_map_2.map | ||||||||||||
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Annotation | Half map of ewald sphere corrected Refine3D_After_CTFRefine.mrc. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Mycobacterium phage Patience
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Mycobacterium phage Patience
Supramolecule | Name: Mycobacterium phage Patience / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1074308 / Sci species name: Mycobacterium phage Patience / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 760.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: gp_4 (capsid accessory protein)
Macromolecule | Name: gp_4 (capsid accessory protein) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.549938 KDa |
Sequence | String: MANRTVSPST QGVRPAMRQM YNGRNVATRP IPLIVDTSEI RAIMAAAADA RPKTSAVNFP QSGPRPAGAA VVFGTKVSGA PGNVVSNNA ATFAPLTGTQ NFE UniProtKB: Uncharacterized protein |
-Macromolecule #2: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 43.845391 KDa |
Sequence | String: MATKELKIGG VPVFPIFGGT APVRQEGIMT QGDLVTVTSD GIDLNALWNS FAESIAIYNE AMDNLIQLLT YPVTVPVEPV VQIGETTFE EATELGVPRG AGLPIEVFQM GYDLRHYDKR NAYSWMFLAD ADGRQVEAIH DAVLWADKRL VFRKVMEALF D NRTRRANI ...String: MATKELKIGG VPVFPIFGGT APVRQEGIMT QGDLVTVTSD GIDLNALWNS FAESIAIYNE AMDNLIQLLT YPVTVPVEPV VQIGETTFE EATELGVPRG AGLPIEVFQM GYDLRHYDKR NAYSWMFLAD ADGRQVEAIH DAVLWADKRL VFRKVMEALF D NRTRRANI RNQAYNVYPL YNGDGVPPPR FKNNVFDETH SHYVISHNSV VDSSDLEDLM ELLAEHGYSP QAGTQFLLLA NK AETDAIR QFRRGVVNNN GATAGYDFIP SPTQPAMMLP NAEGLLGNQP APTFGGLAVI GSYGFWNIVE EDYIPPGYLV GVG YGGAFN LGNPVGLRQH ANPAMQGLRI IAGNYQRYPL VDGFYARSFG TGVRQRGGAA IMQIKASGAY ECPPIYKKGG GFLV UniProtKB: Capsid protein |
-Macromolecule #3: gp_22 (Minor Capsid Protein)
Macromolecule | Name: gp_22 (Minor Capsid Protein) / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.845107 KDa |
Sequence | String: MALKTKPRWD KYDGYVGNYR GVLGEDIDLD TEANRVLAVG TNSNGAIVVG AGQTGIKGLM IVAVGADIHG AMLDGGINNH AGDPQDVGK HGEITNFQPT VFGRTFGVAI SATEGNVKLA VNGVDTGNIA YDTSAANLKS GIVAVDDGFT ADDFTVTGTA P NFTIVTTR ...String: MALKTKPRWD KYDGYVGNYR GVLGEDIDLD TEANRVLAVG TNSNGAIVVG AGQTGIKGLM IVAVGADIHG AMLDGGINNH AGDPQDVGK HGEITNFQPT VFGRTFGVAI SATEGNVKLA VNGVDTGNIA YDTSAANLKS GIVAVDDGFT ADDFTVTGTA P NFTIVTTR TDVTITASGE GVTVTEATSV AAAGTNYYGH ADGTVNAVKG SDGVYVGHTQ EADRLIVNVK DEED UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 8640 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Amino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde. |
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Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-8giu: |