+Open data
-Basic information
Entry | Database: PDB / ID: 1m4x | ||||||
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Title | PBCV-1 virus capsid, quasi-atomic model | ||||||
Components | PBCV-1 virus capsid | ||||||
Keywords | VIRUS / icosahedral virus capsid / beta barrel / Icosahedral virus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paramecium bursaria Chlorella virus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 28 Å | ||||||
Authors | Nandhagopal, N. / Simpson, A.A. / Gurnon, J.R. / Yan, X. / Baker, T.S. / Graves, M.V. / Van Etten, J.L. / Rossmann, M.G. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2002 Title: The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Authors: Narayanasamy Nandhagopal / Alan A Simpson / James R Gurnon / Xiadong Yan / Timothy S Baker / Michael V Graves / James L Van Etten / Michael G Rossmann / Abstract: Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of ...Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus. | ||||||
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 | 1m4x.cif.gz | 242.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m4x.ent.gz | 275.6 KB | Display | PDB format |
PDBx/mmJSON format | 1m4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m4x_validation.pdf.gz | 374 KB | Display | wwPDB validaton report |
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Full document | 1m4x_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 1m4x_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 1m4x_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m4x ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m4x | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
| x 28
3 |
| x 140
4 |
| x 168
5 |
| x 30
6 |
| x 66
7 |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 45734.891 Da / Num. of mol.: 3 / Fragment: virus capsid / Source method: isolated from a natural source Details: Virus infects chlorella algae, which are symbionts with Paramecium bursaria Source: (natural) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / References: GenBank: 323324, UniProt: P30328*PLUS |
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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: PBCV-1 virus capsid / Type: VIRUS / Details: T=169d quasi-symmetric icosahedron. |
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Details of virus | Host category: ALGAE / Type: VIRION |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: electron microscopy grid - in vitrious ice |
Vitrification | Details: frozen in liquid propane |
Crystal grow | *PLUS Method: cryo electron microscopy |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG/ST |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: inverse of CTF was applied to images | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: polar fourier transform. / Resolution: 28 Å / Details: used Tim Baker's programs PFT, EM3DR, etc. / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Target criteria: rigid body refinement in real space against Lagrangian filtered EM density, using the program SITUS.Each molecule in the icosahedral ASU was refined separately. Details: METHOD--6d search, separately for each symmetry related molecule in the icosahedral ASU. REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | 3D fitting-ID: 1 / Details: 1J5Q or 1M3Y (not exactly as found in pdb entry) / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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