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Yorodumi- PDB-1q3y: NMR structure of the Cys28His mutant (D form) of the nucleocapsid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q3y | ||||||
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Title | NMR structure of the Cys28His mutant (D form) of the nucleocapsid protein NCp7 of HIV-1. | ||||||
Components | GAG protein | ||||||
Keywords | VIRAL PROTEIN / CCHC zinc knuckle / CCHH zinc knuckle | ||||||
Function / homology | Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Few Secondary Structures / Irregular / : Function and homology information | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics | ||||||
Authors | Ramboarina, S. / Druillennec, S. / Morellet, N. / Bouaziz, S. / Roques, B.P. | ||||||
Citation | Journal: J.Virol. / Year: 2004 Title: Target specificity of human immunodeficiency virus type 1 NCp7 requires an intact conformation of its CCHC N-terminal zinc finger. Authors: Ramboarina, S. / Druillennec, S. / Morellet, N. / Bouaziz, S. / Roques, B.P. #1: Journal: Biochemistry / Year: 1999 Title: Structural investigation on the requirement of CCHH zinc finger type in nucleocapsid protein of human immunodeficiency virus 1. Authors: Ramboarina, S. / Morellet, N. / Fournie-Zaluski, M.C. / Roques, B.P. | ||||||
History |
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Remark 999 | SEQUENCE The sequence here corresponds to a strain different than that found in the sequence ...SEQUENCE The sequence here corresponds to a strain different than that found in the sequence database (GenBank accession CAB98186). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q3y.cif.gz | 23.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q3y.ent.gz | 14.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q3y_validation.pdf.gz | 292.9 KB | Display | wwPDB validaton report |
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Full document | 1q3y_full_validation.pdf.gz | 292.8 KB | Display | |
Data in XML | 1q3y_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 1q3y_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3y ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4872.646 Da / Num. of mol.: 1 / Fragment: RESIDUES 390-431 / Mutation: C28H / Source method: obtained synthetically Details: Two peptides have been chemically synthesized with and without a 15N/13C labelled Histidine residue at position 28 References: UniProt: Q9PY17 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using standard 2D homonuclear experiments and 1H-15N HSQC experiments. |
-Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics Software ordinal: 1 Details: The structure has been calculated using 335 NOE derived distance restraints. | ||||||||||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 1 |