+Open data
-Basic information
Entry | Database: PDB / ID: 4bp7 | |||||||||
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Title | Asymmetric structure of a virus-receptor complex | |||||||||
Components | COAT PROTEIN | |||||||||
Keywords | VIRUS / BACTERIOPHAGE | |||||||||
Function / homology | Function and homology information negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ENTEROBACTERIA PHAGE MS2 (virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 39 Å | |||||||||
Authors | Dent, K.C. / Thompson, R. / Barker, A.M. / Barr, J.N. / Hiscox, J.A. / Stockley, P.G. / Ranson, N.A. | |||||||||
Citation | Journal: Structure / Year: 2013 Title: The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release. Authors: Kyle C Dent / Rebecca Thompson / Amy M Barker / Julian A Hiscox / John N Barr / Peter G Stockley / Neil A Ranson / Abstract: Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their ...Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection. | |||||||||
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 | 4bp7.cif.gz | 4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4bp7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4bp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bp7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4bp7_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4bp7_validation.xml.gz | 367.1 KB | Display | |
Data in CIF | 4bp7_validation.cif.gz | 662.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/4bp7 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/4bp7 | HTTPS FTP |
-Related structure data
Related structure data | 2365MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 13738.464 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Source: (natural) ENTEROBACTERIA PHAGE MS2 (virus) / References: UniProt: P03612 |
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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: MS2 BOUND TO F-PILUS / Type: COMPLEX |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE HOME MADE FREEZING DEVICE |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 12 / Date: Jan 1, 2012 |
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Electron gun | Electron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 23000 X / Calibrated magnification: 23000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 3000 nm |
Specimen holder | Tilt angle max: 60 ° / Tilt angle min: -60 ° |
Image recording | Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k) |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 39 Å / Num. of particles: 1500 / Nominal pixel size: 9.12 Å / Actual pixel size: 9.12 Å Details: THREE COORDINATE FILES (4BP4, 4BP5, 4BP6) LINKED TO 1 EM STRUCTURE EMD-2365. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 2MS2 Accession code: 2MS2 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 39 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 39 Å
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