+Open data
-Basic information
Entry | Database: PDB / ID: 8qkh | ||||||
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Title | Neck of phage 812 virion (C6) | ||||||
Components |
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Keywords | VIRUS / phage / neck / portal / connector | ||||||
Function / homology | Non-cytoplasmic protein / Non-cytoplasmic protein / Neck protein / Capsid protein / Baseplate hub assembly protein Function and homology information | ||||||
Biological species | Staphylococcus phage 812 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||
Authors | Cienikova, Z. / Novacek, J. / Fuzik, T. / Benesik, M. / Plevka, P. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: To Be Published Title: Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812 Authors: Cienikova, Z. / Novacek, J. / Siborova, M. / Popelarova, B. / Fuzik, T. / Benesik, M. / Bardy, P. / Plevka, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qkh.cif.gz | 280.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qkh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qkh_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8qkh_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8qkh_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 8qkh_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/8qkh ftp://data.pdbj.org/pub/pdb/validation_reports/qk/8qkh | HTTPS FTP |
-Related structure data
Related structure data | 18462MC 8q01C 8q1iC 8q7dC 8qekC 8qemC 8qgrC 8qjeC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 8 molecules AGNnSsab
#1: Protein | Mass: 33757.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN7 | ||||
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#2: Protein | Mass: 31799.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN9 | ||||
#3: Protein | Mass: 10146.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WZ69 #4: Protein | Mass: 17885.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A0A0U1WIM1 #5: Protein | Mass: 34191.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage 812 (virus) / Strain: K1-420 / References: UniProt: A1YTN6 |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Staphylococcus phage 812 / Type: VIRUS / Details: Purified phage virion / Entity ID: #1-#5 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Staphylococcus phage 812 (virus) / Strain: K1-420 | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Staphylococcus aureus / Strain: CCM 8428 | ||||||||||||||||||||
Virus shell | Diameter: 1100 nm | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % |
-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 magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 49 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 30553 |
Image scans | Width: 4000 / Height: 4000 / Movie frames/image: 16 |
-Processing
EM software |
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Image processing | Details: Frame alignment and dose-weighting with MotionCor2, then contrast inversion and normalization | ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 23947 / Details: Manual particle selection | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21731 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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