[English] 日本語
Yorodumi- PDB-4bml: C-alpha backbone trace of major capsid protein gp39 found in mari... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bml | ||||||
---|---|---|---|---|---|---|---|
Title | C-alpha backbone trace of major capsid protein gp39 found in marine virus Syn5. | ||||||
Components | MAJOR CAPSID PROTEIN | ||||||
Keywords | VIRUS / MARINE VIRUS / OUTER CAPSID PROTEIN / MATURATION | ||||||
Function / homology | Major capsid protein Function and homology information | ||||||
Biological species | SYNECHOCOCCUS PHAGE SYN5 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G | ||||||
Authors | Gipson, P. / Baker, M.L. / Raytcheva, D. / Haase-Pettingell, C. / Piret, J. / King, J. / Chiu, W. | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Protruding knob-like proteins violate local symmetries in an icosahedral marine virus. Authors: Preeti Gipson / Matthew L Baker / Desislava Raytcheva / Cameron Haase-Pettingell / Jacqueline Piret / Jonathan A King / Wah Chiu / Abstract: Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by ...Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4bml.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bml.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bml_validation.pdf.gz | 833.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bml_full_validation.pdf.gz | 841.7 KB | Display | |
Data in XML | 4bml_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 4bml_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bml ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bml | HTTPS FTP |
-Related structure data
Related structure data | 5954MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 60||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| x 5||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| x 6||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|