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- PDB-2mqv: Solution NMR structure of the U5-primer binding site (U5-PBS) dom... -

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Basic information

Entry
Database: PDB / ID: 2mqv
TitleSolution NMR structure of the U5-primer binding site (U5-PBS) domain of murine leukemia virus RNA genome bound to the retroviral nucleocapsid protein
Components
  • Nucleocapsid protein p10
  • RNA (68-MER)
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 / 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
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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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 detailsfewest violations, model1
AuthorsD'Souza, V.M. / 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
DepositionJun 27, 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
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein p10
B: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3373
Polymers28,2712
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1409 Å2
ΔGint-4.7 kcal/mol
Surface area18862 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

#1: Protein Nucleocapsid protein p10


Mass: 6377.248 Da / Num. of mol.: 1
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 RNA (68-MER)


Mass: 21893.887 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.: 1 / 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-1H NOESY
1212D 1H-13C HSQC
1312D 1H-13C HSQC
1412D 1H-13C HSQC
1512D 1H-13C HSQC
1632D 1H-1H NOESY
1722D 1H-1H NOESY
1812D 1H-1H NOESY
2932D 1H-1H NOESY
11013D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM 15N,13C-Alab U5-PBS-NC, 0.5 mM 15N.13C-Glab U5-PBS-NC, 0.5 mM 15N.13C-Ulab U5-PBS-NC, 0.5 mM 15N.13C-Clab U5-PBS-NC, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM U5-PBS-M2-NC, 100% D2O100% D2O
31 mM UAUCG-linker, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMU5-PBS-NC-115N,13C-Alab1
0.5 mMU5-PBS-NC-215N.13C-Glab1
0.5 mMU5-PBS-NC-315N.13C-Ulab1
0.5 mMU5-PBS-NC-415N.13C-Clab1
0.5 mMU5-PBS-M2-NC-52
1 mMUAUCG-linker-63
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM Tris, 10mM Nacl 7.0 ambient 311 K
210mM Tris, 10mM NaCl 7.0 ambient 288 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
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CYANAJohnson, One Moon Scientificrefinement
CYANAJohnson, One Moon Scientificdata analysis
CYANAJohnson, One Moon Scientificprocessing
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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