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Yorodumi- PDB-6h9c: Cryo-EM structure of archaeal extremophilic internal membrane-con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h9c | |||||||||||||||
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Title | Cryo-EM structure of archaeal extremophilic internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) at 3.74 Angstroms resolution. | |||||||||||||||
Components |
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Keywords | VIRUS / vertical single beta-barrel virus / internal membrane-containing archaeal virus. | |||||||||||||||
Function / homology | VP7 / VP4 / VP9 Function and homology information | |||||||||||||||
Biological species | Haloarcula californiae ATCC 33799 (Halophile) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.74 Å | |||||||||||||||
Authors | Abrescia, N.G. / Santos-Perez, I. / Charro, D. | |||||||||||||||
Funding support | Spain, Finland, 4items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural basis for assembly of vertical single β-barrel viruses. Authors: Isaac Santos-Pérez / Diego Charro / David Gil-Carton / Mikel Azkargorta / Felix Elortza / Dennis H Bamford / Hanna M Oksanen / Nicola G A Abrescia / Abstract: The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The ...The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6h9c.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6h9c.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6h9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h9c_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6h9c_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6h9c_validation.xml.gz | 160.8 KB | Display | |
Data in CIF | 6h9c_validation.cif.gz | 231.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9c ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9c | HTTPS FTP |
-Related structure data
Related structure data | 0174MC 0050C 0072C 0073C 0131C 0172C 6h82C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 30 molecules DFERTSWKJMNILaYbcdZABCPQOVUHGX
#1: Protein | Mass: 19912.832 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) Plasmid details: Haloarcula californiae icosahedral virus 1 / References: UniProt: A0A1C7A3R1 #2: Protein | | Mass: 16271.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) References: UniProt: A0A1C7A3R7 #3: Protein | | Mass: 9209.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) #4: Protein | | Mass: 6400.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) Plasmid details: Haloarcula californiae icosahedral virus 1 #7: Protein | Mass: 25995.318 Da / Num. of mol.: 12 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) Plasmid details: Haloarcula californiae icosahedral virus 1 / References: UniProt: A0A1C7A3R2 |
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-Protein/peptide , 2 types, 2 molecules ef
#5: Protein/peptide | ( Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) Plasmid details: Haloarcula californiae icosahedral virus 1 |
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#6: Protein/peptide | Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Haloarcula californiae ATCC 33799 (Halophile) |
-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: Haloarcula californiae icosahedral virus 1 / Type: VIRUS / Details: Haloarcula californiae icosahedral virus - 1 / Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Haloarcula californiae icosahedral virus 1 | ||||||||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION | ||||||||||||||||||||||||||||||
Natural host | Organism: Haloarcula californiae ATCC 33799 | ||||||||||||||||||||||||||||||
Virus shell | Diameter: 800 nm / Triangulation number (T number): 28 | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Haloarcula californiae icosahedral virus 1. Taxonomic identifier 1735722 NCBI. | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
-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: 3900 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 36 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3218 |
Image scans | Movie frames/image: 27 / Used frames/image: 1-26 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4584 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3414 / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 89.1 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient Details: The HCIV-1 VP7 and VP4 MCPs were manually built aided by beta-barrel core templates derived from the crystal structures of Thermus bacteriophage P23-77 MCPs (PDB ID 3ZN6). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.74 Å |