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Basic information
| Entry | Database: PDB / ID: 8ckb | ||||||||||||
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| Title | Asymmetric reconstruction of the crAss001 virion | ||||||||||||
 Components |
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 Keywords | VIRUS / crassvirus / crassphage / bacteriophage / phage / podovirus | ||||||||||||
| Function / homology |  Function and homology informationviral capsid, decoration / virus tail / biological process involved in interaction with host / host cell membrane / viral life cycle / virion component / viral capsid / symbiont entry into host cell / virion attachment to host cell / membrane Similarity search - Function | ||||||||||||
| Biological species |  Bacteroides phage crAss001 (virus) | ||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.39 Å | ||||||||||||
 Authors | Bayfield, O.W. / Shkoporov, A.N. / Yutin, N. / Khokhlova, E.V. / Smith, J.L.R. / Hawkins, D.E.D.P. / Koonin, E.V. / Hill, C. / Antson, A.A. | ||||||||||||
| Funding support |  United Kingdom, 1items
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 Citation | Journal: Nature Title: Structural atlas of the most abundant human gut virus Authors: Bayfield, O.W. / Shkoporov, A.N. / Yutin, N. / Khokhlova, E.V. / Smith, J.L.R. / Hawkins, D.E.D.P. / Koonin, E.V. / Hill, C. / Antson, A.A. | ||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: MolmilJmol/JSmol |
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Downloads & links
-Download
| PDBx/mmCIF format | 8ckb.cif.gz | 80.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb8ckb.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 8ckb.json.gz | Tree view | PDBx/mmJSON format | |
| Others |  Other downloads |
-Validation report
| Summary document | 8ckb_validation.pdf.gz | 292.7 KB | Display | wwPDB validaton report |
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| Full document | 8ckb_full_validation.pdf.gz | 290.7 KB | Display | |
| Data in XML | 8ckb_validation.xml.gz | 671 B | Display | |
| Data in CIF | 8ckb_validation.cif.gz | 306 B | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/8ckbftp://data.pdbj.org/pub/pdb/validation_reports/ck/8ckb | HTTPS FTP |
-Related structure data
| Related structure data | M: map data used to model this data |
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| Similar structure data |
-Links
PDBj-
Assembly
| Deposited unit | 
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| 1 |
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-Components
-Protein , 8 types, 1232 molecules A001A002A003A004A005A006A007A008A009A010A011A012A013A014A015A016A017A018A019A020A021A022A023A024A025A026A027A028A029A030...
| #1: Protein | Mass: 36154.094 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVS7#4: Protein | Mass: 10294.763 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus)#6: Protein | Mass: 57098.598 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVU6#7: Protein | Mass: 156459.312 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVD6#8: Protein | Mass: 90913.836 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DV85#9: Protein | Mass: 93122.211 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT68#10: Protein | Mass: 11327.080 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTA3#15: Protein | Mass: 92401.672 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVT1 |
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-Head fiber dimer protein ... , 2 types, 111 molecules A511B001B002B003B004B005B006B007B008B009B010B011B012B013B014B015B016B017B018B019B020B021B022B023B024B025B026B027B028B029...
| #2: Protein/peptide | Mass: 2531.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVL5 |
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| #3: Protein | Mass: 13110.960 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTC5 |
-Ring protein ... , 4 types, 60 molecules J001J002J003J004J005J006J007J008J009J010J011J012K001K002K003K004K005K006K007K008K009K010K011K012L001L002L003L004L005L006...
| #11: Protein | Mass: 27479.625 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT91#12: Protein | Mass: 26216.832 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DT87#13: Protein | Mass: 26076.506 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DV73#14: Protein | Mass: 26680.965 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVC3 |
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-Tail hub protein ... , 2 types, 36 molecules P001P002P003P004P005P006P007P008P009P010P011P012P013P014P015P016P017P018P019P020P021P022P023P024Q001Q002Q003Q004Q005Q006...
| #16: Protein | Mass: 24813.201 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DTH1#17: Protein | Mass: 13411.116 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) / References: UniProt: A0A385DVM6 |
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-Protein/peptide / Non-polymers , 2 types, 88 molecules D001D002D003D004D005D006
| #18: Chemical | ChemComp-MG /  Mass: 24.305 Da / Num. of mol.: 82 / Source method: obtained synthetically / Formula: Mg#5: Protein/peptide | Mass: 1209.482 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bacteroides phage crAss001 (virus) |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: Bacteroides phage crAss001 / Type: VIRUS / Entity ID: #1-#3, #5-#17 / Source: NATURAL | ||||||||||||||||||||
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| Molecular weight | Value: 61 MDa / Experimental value: NO | ||||||||||||||||||||
| Source (natural) | Organism: Bacteroides phage crAss001 (virus) | ||||||||||||||||||||
| Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION | ||||||||||||||||||||
| Natural host | Organism: Bacteroides intestinalis | ||||||||||||||||||||
| Virus shell | Name: Capsid / Diameter: 880 nm / Triangulation number (T number): 9 | ||||||||||||||||||||
| Buffer solution | pH: 7.5 | ||||||||||||||||||||
| Buffer component |
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| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
| Specimen support | Grid material: COPPER | ||||||||||||||||||||
| Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: FEI TITAN KRIOS |
| Electron gun | Electron source:  FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 300 nm |
| Image recording | Electron dose: 51 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
| Software | Name: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package |
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| EM software | Name: EPU / Category: image acquisition |
| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
| 3D reconstruction | Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27445 / Symmetry type: POINT |
