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- PDB-1bj6: 1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1bj6
Title1H NMR OF (12-53) NCP7/D(ACGCC) COMPLEX, 10 STRUCTURES
Components
  • DNA (5'-D(*AP*CP*GP*CP*C)-3')
  • NUCLEOCAPSID PROTEIN 7
KeywordsViral protein/DNA / COMPLEX (NUCLEOCAPSID PROTEIN-DNA) / NUCLEIC ACID / RETROVIRUS / VIRUS MORPHOGENESIS / ZINC FINGER / Viral protein-DNA COMPLEX
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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.
Similarity search - Domain/homology
DNA / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING
AuthorsDemene, H. / Morellet, N. / Teilleux, V. / Huynh-Dinh, T. / De Rocquigny, H. / Fournie-Zaluski, M.C. / Roques, B.P.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Structure of the complex between the HIV-1 nucleocapsid protein NCp7 and the single-stranded pentanucleotide d(ACGCC).
Authors: Morellet, N. / Demene, H. / Teilleux, V. / Huynh-Dinh, T. / de Rocquigny, H. / Fournie-Zaluski, M.C. / Roques, B.P.
History
DepositionJul 3, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / 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_database_status.process_site / _pdbx_nmr_software.name / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_ins_code / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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
D: DNA (5'-D(*AP*CP*GP*CP*C)-3')
A: NUCLEOCAPSID PROTEIN 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4334
Polymers6,3032
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)10 / 50LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY
Representative

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Components

#1: DNA chain DNA (5'-D(*AP*CP*GP*CP*C)-3')


Mass: 1465.001 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide NUCLEOCAPSID PROTEIN 7 / (12-53)NCP7


Mass: 4837.642 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: MAL / References: UniProt: Q74084
#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
111NOESY
121TOCSY
131DQF

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Sample preparation

DetailsContents: WATER
Sample conditionsIonic strength: LOW SALT CONDITIONS / pH: 6 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DiscoverBIOSYMrefinement
BRUKER DISNMRDISNMRstructure solution
BIOSYM/MSIstructure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING / Software ordinal: 1
Details: THE PROTEIN PART OF THE STRUCTURE WAS FIRST GENERATED USING A RESTRAINTED DYNAMICAL ANNEALING CALCULATION. THE D(ACGCC) NUCLEIC ACID UNDER A DNA CONFORMATION WAS DOCKED APPROXIMATIVELY TO ...Details: THE PROTEIN PART OF THE STRUCTURE WAS FIRST GENERATED USING A RESTRAINTED DYNAMICAL ANNEALING CALCULATION. THE D(ACGCC) NUCLEIC ACID UNDER A DNA CONFORMATION WAS DOCKED APPROXIMATIVELY TO THE PROTEIN BASED ON THE 28 INTERMOLECULAR NOES. THE DOCKED STRUCTURE WAS ENERGY-MINIMIZED UNDER NOES RESTRAINTS. THIS INITIAL COMPLEXED STRUCTURE WAS THEN USED FOR A SECOND SET OF SIMULATED ANNEALING CALCULATION.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND LOWEST TOTAL ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 10

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