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- PDB-1wwf: NMR Structure Determined for MLV NC Complex with RNA Sequence CCUCCGU -

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Basic information

Entry
Database: PDB / ID: 1wwf
TitleNMR Structure Determined for MLV NC Complex with RNA Sequence CCUCCGU
Components
  • 5'-R(P*CP*CP*UP*CP*CP*GP*U)-3'
  • Nucleoprotein p10
KeywordsViral protein/RNA / Hydrophobic Guanosine Binding pocket / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


host cell uropod / host cell late endosome membrane / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / 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 / Retroviral matrix protein ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / 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 / 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.
Similarity search - Domain/homology
RNA / Gag polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodSOLUTION NMR / distance geometry
AuthorsDey, A. / York, D. / Smalls-Mantey, A. / Summers, M.F.
CitationJournal: Biochemistry / Year: 2005
Title: Composition and sequence-dependent binding of RNA to the nucleocapsid protein of Moloney murine leukemia virus(,)
Authors: Dey, A. / York, D. / Smalls-Mantey, A. / Summers, M.F.
History
DepositionJan 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Advisory
Revision 1.4May 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_nmr_spectrometer / 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_nmr_spectrometer.model / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-R(P*CP*CP*UP*CP*CP*GP*U)-3'
A: Nucleoprotein p10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5763
Polymers8,5112
Non-polymers651
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 / 40target function
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(P*CP*CP*UP*CP*CP*GP*U)-3'


Mass: 2133.307 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Nucleoprotein p10 / Nucleocapsid Protein


Mass: 6377.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03332
#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 NOESY
1222D NOESY
1312D TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
1Unlabelled RNA: 1mM RNA concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME99.99% D2O
2Unlabelled NC Protein: 1mM protein concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME99.99% D2O
Sample conditionsIonic strength: 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2
pH: 7.0 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Brukercollection
NMRPipeCurrentDelaglio, F. et.alprocessing
RefinementMethod: distance geometry / Software ordinal: 1
Details: The structures are based on a total of following restraints for: RNA:35 intraresidue restraints,37 intermolecular NOE restraints and 12 inter-molecular H-Bond restraints; NC Protein: 22 ...Details: The structures are based on a total of following restraints for: RNA:35 intraresidue restraints,37 intermolecular NOE restraints and 12 inter-molecular H-Bond restraints; NC Protein: 22 intraresidue restraints and 40 H-Bond restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 20

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