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- PDB-2ihx: Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein... -

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Basic information

Entry
Database: PDB / ID: 2ihx
TitleSolution Structure of the Rous Sarcoma Virus Nucleocapsid Protein:uPsi RNA Packaging Signal Complex
Components
  • Nucleocapsid (NC) Protein
  • uPsi RNA
KeywordsVIRAL PROTEIN/RNA / Protein-RNA complex / VIRAL PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


host cell nucleoplasm / viral procapsid maturation / virion component => GO:0044423 / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral process / viral capsid / nucleic acid binding / structural constituent of virion / aspartic-type endopeptidase activity ...host cell nucleoplasm / viral procapsid maturation / virion component => GO:0044423 / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral process / viral capsid / nucleic acid binding / structural constituent of virion / aspartic-type endopeptidase activity / host cell plasma membrane / proteolysis / zinc ion binding / membrane
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Retroviral nucleocapsid Gag protein p24, N-terminal / Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Retroviral nucleocapsid Gag protein p24, N-terminal / Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Few Secondary Structures / Irregular / 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. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Gag polyprotein / Capsid protein p27, alternate cleaved 1
Similarity search - Component
Biological speciesRous sarcoma virus
MethodSOLUTION NMR / 1H-1H distance restraints, Hydrogen-bond restraints, Torsion angle restraints, Inter-phosphate restraints
AuthorsZhou, J. / Summers, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution Structure of the Rous Sarcoma Virus Nucleocapsid Protein: muPsi RNA Packaging Signal Complex.
Authors: Zhou, J. / Bean, R.L. / Vogt, V.M. / Summers, M.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: uPsi RNA
A: Nucleocapsid (NC) Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1054
Polymers30,9742
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 800structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: RNA chain uPsi RNA


Mass: 24267.391 Da / Num. of mol.: 1
Fragment: minimal RNA packaging signal in the 5'- untranslated region (UTR) of Rous sarcoma virus (RSV)
Source method: obtained synthetically
Details: RNA was prepared by in vitro T7 RNA transcription. The sequence occurs naturally in Rous sarcoma virus (RSV)
#2: Protein Nucleocapsid (NC) Protein


Mass: 6706.681 Da / Num. of mol.: 1 / Fragment: Nucleocapsid domain (residues 503-563)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus / Genus: Alpharetrovirus / Strain: Prague C (Pr-C) / Gene: GAG / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus (DE3)-RIL / References: UniProt: P03322, UniProt: Q77YH0*PLUS
#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 NOESY
1222D NOESY
1332D NOESY
1442D NOESY
1552D NOESY
1663D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM unlabeled nucleocapsid protein, 1.0 mM A-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O100% D2O
21.2 mM unlabeled nucleocapsid protein, 1.2 mM G-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O100% D2O
30.8 mM unlabeled nucleocapsid protein, 0.8 mM U-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O100% D2O
40.8 mM unlabeled nucleocapsid protein, 0.8 mM C-selectively-protonated uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O100% D2O
51.2 mM unlabeled nucleocapsid protein, 1.2 mM unlabeled uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0, 5mM NaCl, 0.1 mM ZnCl2, 100% D2O100% D2O
61.2 mM 15N, 13C-labeled nucleocapsid protein, 1.2 mM unlabeled uPsi RNA, 5 mM Tris-d11-HCl buffer, pH 7.0; 5mM NaCl, 0.1 mM ZnCl2, 100% D2O100% D2O
Sample conditionsIonic strength: 5 mM NaCl, 0.1 mM ZnCl2 / pH: 7.0 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBRUKERcollection
NMRPipeDelaglio, F., Grzesiek. S., Vuister, G.W., Zhu, G., Pfeifer, J., & Bax, A.processing
NMRView5Johnson, B.A., Blevins, R.A.data analysis
CYANA2.1Guntert, P., Mumenthaler, C. & Wuthrich, K.refinement
RefinementMethod: 1H-1H distance restraints, Hydrogen-bond restraints, Torsion angle restraints, Inter-phosphate restraints
Software ordinal: 1
Details: The structures are based on a total of 1697 restraints. 680 are NOE-derived distance restraints, 608 are Hydrogen-bond restraints, 239 are torsion angle restraints and 170 are inter-phosphate restraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 800 / Conformers submitted total number: 20

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