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Yorodumi- PDB-1hvo: ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE N-TER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hvo | ||||||
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Title | ZINC-AND SEQUENCE-DEPENDENT BINDING TO NUCLEIC ACIDS BY THE N-TERMINAL ZINC FINGER DOMAIN OF THE HIV-1 NUCLEOCAPSID PROTEIN: NMR STRUCTURE OF THE COMPLEX WITH THE PSI-SITE ANALOG, D/ACGCC | ||||||
Components |
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Keywords | Viral protein/DNA / DNA / ZINC FINGER DOMAIN / HIV-1 NUCLEOCAPSID PROTEIN / PSI-SITE ANALOG / Viral protein-DNA COMPLEX | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | South, T.L. / Summers, M.F. | ||||||
Citation | Journal: Protein Sci. / Year: 1993 Title: Zinc- and sequence-dependent binding to nucleic acids by the N-terminal zinc finger of the HIV-1 nucleocapsid protein: NMR structure of the complex with the Psi-site analog, dACGCC. Authors: South, T.L. / Summers, M.F. #1: Journal: Protein Sci. / Year: 1992 Title: Nucleocapsid Zinc Fingers Detected in Retroviruses: Exafs Studies of Intact Viruses and the Solution-State Structure of the Nucleocapsid Protein from HIV-1 Authors: Summers, M.F. / Henderson, L.E. / Chance, M.R. / Bess Junior, J.W. / South, T.L. / Blake, P.R. / Sagi, I. / Perez-Alvarado, G. / Sowder III, R.C. / Hare, D.R. / Arthur, L.O. #2: Journal: Biochemistry / Year: 1991 Title: The C-Terminal Retroviral-Type Zinc Finger Domain from the HIV-1 Nucleocapsid Protein is Structurally Similar to the N-Terminal Zinc Finger Domain Authors: South, T.L. / Blake, P.R. / Hare, D.R. / Summers, M.F. #3: Journal: Biochemistry / Year: 1990 Title: The Nucleocapsid Protein Isolated from HIV-I Particles Binds Zinc and Form Retroviral-Type Zinc Fingers Authors: South, T.L. / Blake, P.R. / Sowder, R. / Arthur, L.O. / Henderson, L.E. / Summers, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hvo.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hvo.ent.gz | 112.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/1hvo ftp://data.pdbj.org/pub/pdb/validation_reports/hv/1hvo | HTTPS FTP |
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-Related structure data
-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 / Keywords: DEOXYRIBONUCLEIC ACID |
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#2: Protein/peptide | Mass: 2011.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Keywords: POLYPEPTIDE / References: UniProt: Q70622 |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE AVERAGE PAIRWISE RMDS'S FOR THE 40 DG/SA STRUCTURES (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.42 (0.07) ANGSTROMS. THE AVERAGE RMS DEVIATION FOR THE 40 DG/SA STRUCTURES RELATIVE TO THE MEAN ...Text: THE AVERAGE PAIRWISE RMDS'S FOR THE 40 DG/SA STRUCTURES (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.42 (0.07) ANGSTROMS. THE AVERAGE RMS DEVIATION FOR THE 40 DG/SA STRUCTURES RELATIVE TO THE MEAN COORDINATES (C,CA,N ATOMS OF RESIDUES A1-L51) IS 0.29 (0.07) ANGSTROMS. |
-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
NMR software | Name: DSPACE / Classification: refinement |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE INTERNAL CONFORMATION OF THE OLIGODEOXYRIBONUCLEOTIDE, D(ACGCC), WAS HELD FIXED IN AN IDEALIZED A-HELICAL CONFORMATION. THE A-HELIX STRUCTURE WAS GENERATED WITH QUANTA. SIMULATED ...Details: THE INTERNAL CONFORMATION OF THE OLIGODEOXYRIBONUCLEOTIDE, D(ACGCC), WAS HELD FIXED IN AN IDEALIZED A-HELICAL CONFORMATION. THE A-HELIX STRUCTURE WAS GENERATED WITH QUANTA. SIMULATED ANNEALING WAS PERFORMED IN A MANNER THAT ALLOWED ATOMS OF THE ZINC FINGER ONLY TO MOVE DURING REFINEMENT. |
NMR ensemble | Conformers submitted total number: 15 |