+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40271 | |||||||||
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Title | Mycobacterium phage Adjutor | |||||||||
Map data | Sharpened map of ewald sphere corrected postprocess. | |||||||||
Sample |
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Keywords | T=7 / HK97 / Tailed bacteriophage / Capsid / VIRUS | |||||||||
Function / homology | Uncharacterized protein / Capsid decoration protein / Major capsid protein Function and homology information | |||||||||
Biological species | Mycobacterium phage Adjutor (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
Authors | Podgorski JM / White SJ | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: A novel accessory protein stabilizes the capsid of two actinobacteriophages Authors: Podgorski JM / Podgorski 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 | emd_40271.map.gz | 1.7 GB | EMDB map data format | |
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Header (meta data) | emd-40271-v30.xml emd-40271.xml | 20.6 KB 20.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40271_fsc.xml | 27.9 KB | Display | FSC data file |
Images | emd_40271.png | 293 KB | ||
Masks | emd_40271_msk_1.map | 1.9 GB | Mask map | |
Filedesc metadata | emd-40271.cif.gz | 6 KB | ||
Others | emd_40271_additional_1.map.gz emd_40271_half_map_1.map.gz emd_40271_half_map_2.map.gz | 1.8 GB 1.5 GB 1.5 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40271 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40271 | HTTPS FTP |
-Validation report
Summary document | emd_40271_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_40271_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_40271_validation.xml.gz | 35 KB | Display | |
Data in CIF | emd_40271_validation.cif.gz | 47.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40271 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40271 | HTTPS FTP |
-Related structure data
Related structure data | 8sajMC 8giuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40271.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-Mask #1
File | emd_40271_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Ewald sphere corrected map.
File | emd_40271_additional_1.map | ||||||||||||
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Annotation | Ewald sphere corrected map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of ewald sphere corrected map.
File | emd_40271_half_map_1.map | ||||||||||||
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Annotation | Half map of ewald sphere corrected map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of ewald sphere corrected map.
File | emd_40271_half_map_2.map | ||||||||||||
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Annotation | Half map of ewald sphere corrected map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mycobacterium phage Adjutor
Entire | Name: Mycobacterium phage Adjutor (virus) |
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Components |
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-Supramolecule #1: Mycobacterium phage Adjutor
Supramolecule | Name: Mycobacterium phage Adjutor / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 528321 / Sci species name: Mycobacterium phage Adjutor / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Virus shell | Shell ID: 1 / Diameter: 750.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium phage Adjutor (virus) |
Molecular weight | Theoretical: 45.525645 KDa |
Sequence | String: MKTATEGRVM RESFLEIIAV VGLSGHDNQG GYNTAGDIKY KTADGVSYDS LWNLFSNVTD EWNKHKSKMV QLMTFPVTNQ TEKVPRIGQ FGFEKASEFG VPESKRTELS FYQLAYDFED YDLAFRYTWK FLRDAPSSQI KAYHNQALQA DAKLIHRKVM E AIFDNRER ...String: MKTATEGRVM RESFLEIIAV VGLSGHDNQG GYNTAGDIKY KTADGVSYDS LWNLFSNVTD EWNKHKSKMV QLMTFPVTNQ TEKVPRIGQ FGFEKASEFG VPESKRTELS FYQLAYDFED YDLAFRYTWK FLRDAPSSQI KAYHNQALQA DAKLIHRKVM E AIFDNRER EADIEGLPYK VYPLYNGDNM IPPEYNGTTF STGHNHYLVS GGTKIDSADV EMAADHIREH GYTEENGTQL IA FAHKAEI QEVRRFRFGQ TNNNSAVANY DFVQSQGESP LYLPNADGLL GKQPQSMWKG LRVKGSYDDV LWIEEPTMPA GYV LFLATG GTLAQQNLVG LREHEDAAWR GLRQIPGNQT RYPLIDSFYQ RSFGTGIRQR GGAVVLQIKA SGTYDIPTKW TNGG GFE UniProtKB: Major capsid protein |
-Macromolecule #2: gp_16 (Minor Capsid Protein)
Macromolecule | Name: gp_16 (Minor Capsid Protein) / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium phage Adjutor (virus) |
Molecular weight | Theoretical: 13.766352 KDa |
Sequence | String: MARYDKYNPY GGGFRAPLAA DWTDADAGKL YAVGINNVGA VVKGAGQSGV AGVLVLTKGA KAGSIVDVMK FGEVVEFGPT SGTPGTDFG AAGTAYYADT STGAINSTSG EAKVKVGHTV GAQRLIVAVA DGVVDPSPAA UniProtKB: Capsid decoration protein |
-Macromolecule #3: HNH endonuclease
Macromolecule | Name: HNH endonuclease / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium phage Adjutor (virus) |
Molecular weight | Theoretical: 6.198103 KDa |
Sequence | String: MAKGVKKLPK RKGTNPIPRD KWNSDDIARR QLEQDQKLHL TTKGPHTGTN DSFK UniProtKB: Uncharacterized 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 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) / Detector mode: COUNTING / Number real images: 6664 / 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: 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 |
+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-8saj: |