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- PDB-1a6b: NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP1... -

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Basic information

Entry
Database: PDB / ID: 1a6b
TitleNMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES
Components
  • DNA (5'-D(*AP*CP*GP*CP*C)-3')
  • ZINC FINGER PROTEIN NCP10
KeywordsViral protein/DNA / NUCLEOCAPSID PROTEIN / INTERCALATION / NUCLEIC ACID / RETROVIRUS / ZINC FINGER / Viral protein-DNA 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 / : ...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 / : / Few Secondary Structures / Irregular / 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.
Similarity search - Domain/homology
DNA / Gag polyprotein
Similarity search - Component
MethodSOLUTION NMR / DYNAMICAL SIMULATED ANNEALING, ENERGY MINIMIZATION
AuthorsSchueler, W. / Dong, C.-Z. / Wecker, K. / Roques, B.P.
Citation
Journal: Biochemistry / Year: 1999
Title: NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes.
Authors: Schuler, W. / Dong, C. / Wecker, K. / Roques, B.P.
#1: Journal: J.Biomol.NMR / Year: 1994
Title: Three-Dimensional 1H NMR Structure of the Nucleocapsid Protein Ncp10 of Moloney Murine Leukemia Virus
Authors: Demene, H. / Jullian, N. / Morellet, N. / De Rocquigny, H. / Cornille, F. / Maigret, B. / Roques, B.P.
History
DepositionFeb 23, 1998Processing site: BNL
Revision 1.0Aug 23, 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.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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*GP*CP*C)-3')
B: ZINC FINGER PROTEIN NCP10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2373
Polymers6,1712
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 / 50LEAST RESTRAINT VIOLATIONS, 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 ZINC FINGER PROTEIN NCP10 / MOMULV


Mass: 4706.383 Da / Num. of mol.: 1 / Fragment: CENTRAL DOMAIN RESIDUES 14-53
Source method: isolated from a genetically manipulated source
Details: ONE ZINC ION BOUND IN CCHC BOX / 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
111NOESY
121TOCSY
131E.COSY
141DQF-COSY
NMR detailsText: REPRESENTATIVE MODEL NUMBER: ZINC WAS ADDED IN 1.5EQ AS ZNCL2. THE STRUCTURE WAS DETERMINED USING 1H-NMR SPECTROSCOPY ON THE CENTRAL DOMAIN (14-53)NCP10.

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 293 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 UXNMRUXNMRstructure solution
BIOSYM/MSI FELIXFELIXstructure solution
RefinementMethod: DYNAMICAL SIMULATED ANNEALING, ENERGY MINIMIZATION / Software ordinal: 1
Details: THE PROTEIN PART OF THE STRUCTURE WAS GENERATED IN A SIMULATED ANNEALING CALCULATION AND DOCKED WITH THE NUCLEOTIDE (IDEALIZED CONFORMATION) IN SUCCESSIVE ENERGY MINIMIZATIONS APPLYING FIRST ...Details: THE PROTEIN PART OF THE STRUCTURE WAS GENERATED IN A SIMULATED ANNEALING CALCULATION AND DOCKED WITH THE NUCLEOTIDE (IDEALIZED CONFORMATION) IN SUCCESSIVE ENERGY MINIMIZATIONS APPLYING FIRST INTRA, THEN INTERMOLECULAR NOE RESTRAINTS. THE CONFORMATION OF THE SINGLE STRANDED NUCLEOTIDE GETS DEFINED BY THE CONTACTS TO THE PROTEIN. FIFTY STRUCTURES OF THE COMPLEX WERE GENERATED BY SIMULATED ANNEALING AND ENERGY MINIMIZATION (MAXIMUM GRADIENT O.O2 KCAL/MOL/A2) THE NUCLEOTIDE CONFORMATION WAS KEPT FIXED DURING SIMULATED ANNEALING IN THE CONFORMATION OBTAINED IN THE FIRST STEP. TWENTY STRUCTURES WERE SELECTED WITH RESPECT TO RESTRAINT VIOLATIONS AND TOTAL ENERGY.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS, LOWEST TOTAL ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 20

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