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Yorodumi- PDB-4btq: Coordinates of the bacteriophage phi6 capsid subunits fitted into... -
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-Basic information
Entry | Database: PDB / ID: 4btq | ||||||
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Title | Coordinates of the bacteriophage phi6 capsid subunits fitted into the cryoEM map EMD-1206 | ||||||
Components | MAJOR INNER PROTEIN P1 | ||||||
Keywords | VIRAL PROTEIN / CYSTOVIRIDAE / PROCAPSID STRUCTURE / FLEXIBLE FITTING | ||||||
Function / homology | : / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1 Function and homology information | ||||||
Biological species | PSEUDOMONAS PHAGE PHI6 (bacteriophage) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||
Authors | Nemecek, D. / Boura, E. / Wu, W. / Cheng, N. / Plevka, P. / Qiao, J. / Mindich, L. / Heymann, J.B. / Hurley, J.H. / Steven, A.C. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Subunit folds and maturation pathway of a dsRNA virus capsid. Authors: Daniel Nemecek / Evzen Boura / Weimin Wu / Naiqian Cheng / Pavel Plevka / Jian Qiao / Leonard Mindich / J Bernard Heymann / James H Hurley / Alasdair C Steven / Abstract: The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits ...The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits in its icosahedral capsid, and capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with an α-helical fold. We also solved the procapsid with cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation that is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4btq.cif.gz | 200.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4btq.ent.gz | 120.4 KB | Display | PDB format |
PDBx/mmJSON format | 4btq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4btq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4btq_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4btq_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 4btq_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/4btq ftp://data.pdbj.org/pub/pdb/validation_reports/bt/4btq | HTTPS FTP |
-Related structure data
Related structure data | 1206M 2364C 4btgC 4k7hC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
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-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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