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- PDB-2ms1: Solution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) ... -

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Basic information

Entry
Database: PDB / ID: 2ms1
TitleSolution NMR structure of tRNApro:MLV Nucleocapsid Protein (1:1) Complex
Components
  • Nucleocapsid protein p10
  • tRNApro
KeywordsVIRAL PROTEIN/RNA / RNA/PROTEIN / VIRAL PROTEIN-RNA complex / RETROVIRAL PRIMER ANNEALING / NUCLEOCAPSID CHAPERONE
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / Zinc knuckle
Similarity search - Domain/homology
RNA / RNA (> 10) / Antitermination protein
Similarity search - Component
Biological speciesMurine leukemia virus
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
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 10, 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_nmr_software / 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_nmr_software.name / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,3873
Polymers29,3222
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1386 Å2
ΔGint-5.7 kcal/mol
Surface area18620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the least restraint violations
RepresentativeModel #1lowest energy

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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 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.: 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-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1412D 1H-13C HSQC
1512D 1H-13C HSQC
1612D 1H-13C HSQC
1712D NOESY
1812D NOESY
1912D NOESY
11012D 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-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
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-pro13C1
0.5 mMNC-tRNApro (1:1)-413C, 15N G-lab tRNA-pro1
0.5 mMNC-tRNApro (1:1)-513C, 15N G-lab tRNA-13C1
0.5 mMNC-tRNApro (1:1)-613C, 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 Kollmandata analysis
AmberJohnson, One Moon Scientificdata analysis
AmberDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
Amberrefinement
CYANArefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 10

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