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- PDB-2ms1: Solution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ms1 | ||||||
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Title | Solution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) Complex | ||||||
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![]() | VIRAL PROTEIN/RNA / RNA/PROTEIN / VIRAL PROTEIN-RNA complex / RETROVIRAL PRIMER ANNEALING / NUCLEOCAPSID CHAPERONE | ||||||
Function / homology | ![]() retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / distance geometry | ||||||
Model details | lowest energy, model1 | ||||||
![]() | D'Souza, V. / Yildiz, Z. | ||||||
![]() | ![]() Title: A structure-based mechanism for tRNA and retroviral RNA remodelling during primer annealing. Authors: Miller, S.B. / Yildiz, F.Z. / Lo, J.A. / Wang, B. / D'Souza, V.M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 627.1 KB | Display | ![]() |
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PDB format | ![]() | 518.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 416.1 KB | Display | ![]() |
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Full document | ![]() | 553.9 KB | Display | |
Data in XML | ![]() | 30.6 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2mqtC ![]() 2mqvC ![]() 2ms0C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 6377.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: RNA chain | Mass: 22944.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) ![]() |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.5 mM NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro13C NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, ...Contents: 0.5 mM NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro13C NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-13C NC-tRNApro (1:1), 0.5 mM 13C, 15N G-lab tRNA-pro NC-tRNApro (1:1), 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 10mM Tris, 1mM MgCl2, 10mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 311 K |
-NMR measurement
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz |
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Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 20 / Conformers submitted total number: 10 |