+Open data
-Basic information
Entry | Database: PDB / ID: 6r3b | ||||||
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Title | BACTERIOPHAGE SPP1 PROCAPSID-I PROTEIN | ||||||
Components | Major capsid protein | ||||||
Keywords | VIRUS | ||||||
Function / homology | Major capsid protein 13-like / Major capsid protein 13-like / T=7 icosahedral viral capsid / viral capsid / Major capsid protein Function and homology information | ||||||
Biological species | Bacillus phage SPP1 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Ignatiou, A. / Brasiles, S. / El Sadek-Fadel, M. / Buerger, J. / Mielke, T. / Topf, M. / Tavares, P. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Structural transitions during the scaffolding-driven assembly of a viral capsid. Authors: Athanasios Ignatiou / Sandrine Brasilès / Mehdi El Sadek Fadel / Jörg Bürger / Thorsten Mielke / Maya Topf / Paulo Tavares / Elena V Orlova / Abstract: Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid ...Assembly of tailed bacteriophages and herpesviruses starts with formation of procapsids (virion precursors without DNA). Scaffolding proteins (SP) drive assembly by chaperoning the major capsid protein (MCP) to build an icosahedral lattice. Here we report near-atomic resolution cryo-EM structures of the bacteriophage SPP1 procapsid, the intermediate expanded procapsid with partially released SPs, and the mature capsid with DNA. In the intermediate state, SPs are bound only to MCP pentons and to adjacent subunits from hexons. SP departure results in the expanded state associated with unfolding of the MCP N-terminus and straightening of E-loops. The newly formed extensive inter-capsomere bonding appears to compensate for release of SPs that clasp MCP capsomeres together. Subsequent DNA packaging instigates bending of MCP A domain loops outwards, closing the hexons central opening and creating the capsid auxiliary protein binding interface. These findings provide a molecular basis for the sequential structural rearrangements during viral capsid maturation. | ||||||
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 | 6r3b.cif.gz | 376.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r3b.ent.gz | 299.1 KB | Display | PDB format |
PDBx/mmJSON format | 6r3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r3b_validation.pdf.gz | 890.9 KB | Display | wwPDB validaton report |
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Full document | 6r3b_full_validation.pdf.gz | 901.3 KB | Display | |
Data in XML | 6r3b_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 6r3b_validation.cif.gz | 91.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/6r3b ftp://data.pdbj.org/pub/pdb/validation_reports/r3/6r3b | HTTPS FTP |
-Related structure data
Related structure data | 4717MC 4716C 6r3aC 6rtlC 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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-Components
#1: Protein | Mass: 35258.426 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bacillus phage SPP1 (virus) / References: UniProt: Q38582 |
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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: Bacillus phage SPP1 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 30 MDa / Experimental value: NO |
Source (natural) | Organism: Bacillus phage SPP1 (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Bacillus subtilis |
Virus shell | Name: procapsid / Diameter: 550 nm / Triangulation number (T number): 7 |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3/3 |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 39000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 2500 nm / Cs: 2.3 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Temperature (max): 70 K / Temperature (min): 60 K |
Image recording | Average exposure time: 5 sec. / Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7000 / Details: Movie frames were aligned using MOTIONCORR-2 |
EM imaging optics | Chromatic aberration corrector: none / Spherical aberration corrector: none |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 |
-Processing
EM software |
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CTF correction | Details: Assessment of the contrast transfer function of the microscope was done using CTFFIND4 Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6078 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4558 / Algorithm: EXACT BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4AN5 Accession code: 4AN5 / Source name: PDB / Type: experimental model |