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Yorodumi- PDB-5m1h: Structure of a Spumaretrovirus Gag central domain reveals an anci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m1h | ||||||
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Title | Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid | ||||||
Components | Gag proteinHIV-1 protease | ||||||
Keywords | VIRAL PROTEIN / GAG / FOAMY VIRUS | ||||||
Function / homology | Function and homology information host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral budding via host ESCRT complex / viral release from host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Human spumaretrovirus | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Taylor, I.A. / Nicastro, G. / Ball, N. | ||||||
Citation | Journal: Plos Pathog. / Year: 2016 Title: Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid. Authors: Ball, N.J. / Nicastro, G. / Dutta, M. / Pollard, D.J. / Goldstone, D.C. / Sanz-Ramos, M. / Ramos, A. / Mullers, E. / Stirnnagel, K. / Stanke, N. / Lindemann, D. / Stoye, J.P. / Taylor, W.R. ...Authors: Ball, N.J. / Nicastro, G. / Dutta, M. / Pollard, D.J. / Goldstone, D.C. / Sanz-Ramos, M. / Ramos, A. / Mullers, E. / Stirnnagel, K. / Stanke, N. / Lindemann, D. / Stoye, J.P. / Taylor, W.R. / Rosenthal, P.B. / Taylor, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m1h.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5m1h.ent.gz | 896.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/5m1h ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m1h | HTTPS FTP |
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-Related structure data
Related structure data | 5m1gC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19604.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human spumaretrovirus / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: P14349 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution / Contents: 0.3 mM [U-13C; U-15N] protein, 95% H2O/5% D2O / Label: 13C,15N_sample / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 0.3 mM / Component: protein / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 20mM NaCl, 20mM Tris mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 Pa / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 | |||||||||
NMR representative | Selection criteria: lowest energy | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |