- PDB-2jzw: How the HIV-1 nucleocapsid protein binds and destabilises the (-)... -
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Basic information
Entry
Database: PDB / ID: 2jzw
Title
How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription
Components
DNA (5'-D(*DGP*DTP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DCP*DGP*DGP*DGP*DC)-3')
HIV-1 nucleocapsid protein NCp7(12-55)
Keywords
VIRAL PROTEIN/DNA / human immunodeficiency virus type 1 (HIV-1) / nuclear magnetic resonance (NMR) / nucleocapsid protein (NCp7) / primer binding site (PBS) / exchange / VIRAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information
HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function
Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
3
BrukerBiospin
collection
XwinNMR
3
BrukerBiospin
processing
Discover
2.98
Accelrys
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR constraints
NOE constraints total: 710 / NOE intraresidue total count: 266 / NOE long range total count: 108 / NOE medium range total count: 72 / NOE sequential total count: 196
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 19
NMR ensemble rms
Distance rms dev: 0.028 Å / Distance rms dev error: 0.006 Å
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