+Open data
-Basic information
Entry | Database: PDB / ID: 1qd3 | |||||||||
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Title | HIV-1 TAR RNA/NEOMYCIN B COMPLEX | |||||||||
Components | HIV-1 TAR RNA | |||||||||
Keywords | RNA / HIV-1 / AMINOGLYCOSIDE-RNA-COMPLEX / MINOR GROOVE BINDING | |||||||||
Function / homology | 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose / 2-DEOXYSTREPTAMINE / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Faber, C. / Sticht, H. / Roesch, P. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B. Authors: Faber, C. / Sticht, H. / Schweimer, K. / Rosch, P. #1: Journal: Biochemistry / Year: 1998 Title: Binding of Neomycin to the Tar Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism Authors: Wang, S. / Huber, P.W. / Mei, C. / Czarnik, A.W. / Mei, H.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qd3.cif.gz | 364.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qd3.ent.gz | 307.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qd3_validation.pdf.gz | 450 KB | Display | wwPDB validaton report |
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Full document | 1qd3_full_validation.pdf.gz | 621.8 KB | Display | |
Data in XML | 1qd3_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1qd3_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qd3 ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qd3 | HTTPS FTP |
-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: RNA chain | Mass: 9308.538 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-45 / Source method: isolated from a natural source Details: NEOMYCIN B (RESIDUES BDG-CYY-RYB-IDG) COMPLEXED IN THE RNA MINOR GROOVE Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: Z2/CDC-Z34 ISOLATE |
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#2: Polysaccharide | 2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-alpha-D-ribofuranose Source method: isolated from a genetically manipulated source |
#3: Sugar | ChemComp-BDG / |
#4: Chemical | ChemComp-CYY / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: D2O |
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Sample conditions | Ionic strength: 110 mM / pH: 6.4 / Pressure: 1 atm / Temperature: 308 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA Conformers calculated total number: 100 / Conformers submitted total number: 17 |