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- PDB-2ms0: Solution NMR structure pf tRNApro:MLV-Nucleocapsid (1:2) Complex -

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Basic information

Entry
Database: PDB / ID: 2ms0
TitleSolution NMR structure pf tRNApro:MLV-Nucleocapsid (1:2) Complex
Components
  • Nucleocapsid protein p10Capsid
  • tRNApro
KeywordsVIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA complex / RETROVIRAL PRIMER ANNEALING / NUCLEOCAPSID CHAPERONE / PRIMER BINDING SITE
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMurine leukemia virus
MethodSOLUTION NMR / distance geometry
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsD'Souza, V. / Yildiz, Z.
CitationJournal: Nature / Year: 2014
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.
History
DepositionJul 19, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Nucleocapsid protein p10
B: tRNApro
C: Nucleocapsid protein p10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8305
Polymers35,6993
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4576 Å2
ΔGint-20.7 kcal/mol
Surface area22366 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein Nucleocapsid protein p10 / Capsid


Mass: 6377.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine leukemia virus / Production host: Escherichia coli (E. coli) / References: UniProt: P03355
#2: RNA chain tRNApro


Mass: 22944.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Murine leukemia virus
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1412D 1H-13C HSQC
1512D 1H-13C HSQC
1612D 1H-13C HSQC
1712D NOESY

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Sample preparation

DetailsContents: 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-pro NC-tRNApro (1:1), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMNC-tRNApro (1:1)-11
0.5 mMNC-tRNApro (1:1)-213C, 15N G-lab tRNA-pro1
0.5 mMNC-tRNApro (1:1)-313C, 15N G-lab tRNA-pro1
Sample conditionsIonic strength: 10mM Tris, 1mM MgCl2, 10mM NaCl / pH: 7.2 / Pressure: ambient / Temperature: 311 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmandata analysis
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanprocessing
AMBERJohnson, One Moon Scientificrefinement
AMBERJohnson, One Moon Scientificdata analysis
AMBERJohnson, One Moon Scientificprocessing
AMBERDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
AMBERDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
AMBERDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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