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Yorodumi- PDB-1l6n: STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l6n | ||||||
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Title | STRUCTURE OF THE N-TERMINAL 283-RESIDUE FRAGMENT OF THE HIV-1 GAG POLYPROTEIN | ||||||
Components | Gag Polyprotein | ||||||
Keywords | VIRAL PROTEIN / gag / matrix / capsid / maturation | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / structural molecule activity / virion membrane / RNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Tang, C. / Ndassa, Y. / Summers, M.F. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structure of the N-terminal 283-residue fragment of the immature HIV-1 Gag polyprotein. Authors: Tang, C. / Ndassa, Y. / 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 | 1l6n.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1l6n.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 1l6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l6n_validation.pdf.gz | 351 KB | Display | wwPDB validaton report |
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Full document | 1l6n_full_validation.pdf.gz | 619.5 KB | Display | |
Data in XML | 1l6n_validation.xml.gz | 145.1 KB | Display | |
Data in CIF | 1l6n_validation.cif.gz | 183 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/1l6n ftp://data.pdbj.org/pub/pdb/validation_reports/l6/1l6n | 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 | Mass: 32392.873 Da / Num. of mol.: 1 / Fragment: Residues 1-283 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: gag / Plasmid: p11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q72497 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 50 / pH: 5 / Pressure: 1 atm / Temperature: 303 K | |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANNEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT ...Details: 20 CONFORMERS COMPATIBLE WITH THE NMR CONSTRAINTS WERE CALCULATED USING DYANA 1.5 AND THE STANDARD TORSION ANGLE SIMULATED ANNEALING PROTOCOL. PRELIMINARY CALCULATIONS WERE CARRIED OUT INDEPENDENTLY FOR MATRIX AND CAPSID N-TERMINAL DOMAINS OF THE PROTEIN. INITIALLY ONLY NOE DISTANCE CONSTRAINTS WERE IMPOSED. UNAMBIGUOUS H-BONDS WERE ALSO INCORPORATED TO REINFORCE CANONICAL SECONDARY STRUCTURE. THE INITIAL STRUCTURES WERE THEN USED TO ASSESS THE ACCURACY OF THE TORSION ANGLE CONSTRAINTS GENERATED BY ANALYSIS OF HA, CA, CB, CO AND N CHEMICAL SHIFTS WITH THE PROGRAM TALOS. FINALLY, ALL THE CONSTRAINTS WERE USED TO CALCULATE THE STRUCTURE OF THE WHOLE PROTEIN. | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |