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Yorodumi- PDB-1a6b: NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a6b | ||||||
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Title | NMR 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 |
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Keywords | Viral 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 | ||||||
Method | SOLUTION NMR / DYNAMICAL SIMULATED ANNEALING, ENERGY MINIMIZATION | ||||||
Authors | Schueler, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6b.cif.gz | 316.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6b.ent.gz | 273.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6b ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6b | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 1465.001 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein/peptide | 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 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: 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. |
-Sample preparation
Sample conditions | pH: 6.5 / Temperature: 293 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: 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 ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATIONS, LOWEST TOTAL ENERGY Conformers calculated total number: 50 / Conformers submitted total number: 20 |