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- PDB-2jzw: How the HIV-1 nucleocapsid protein binds and destabilises the (-)... -

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Basic information

Entry
Database: PDB / ID: 2jzw
TitleHow 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)
KeywordsVIRAL 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


induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase / viral genome integration into host DNA ...induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase / viral genome integration into host DNA / RNA-directed DNA polymerase activity / establishment of integrated proviral latency / Transferases, Transferring phosphorus-containing groups, Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / suppression by virus of host gene expression / viral entry into host cell / viral nucleocapsid / DNA recombination / Hydrolases, Acting on ester bonds / lipid binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / DNA binding / zinc ion binding
Peptidase A2A, retrovirus, catalytic / Reverse transcriptase connection / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase, catalytic core / Zinc finger, CCHC-type / Aspartic peptidase, active site / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain ...Peptidase A2A, retrovirus, catalytic / Reverse transcriptase connection / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase, catalytic core / Zinc finger, CCHC-type / Aspartic peptidase, active site / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Reverse transcriptase thumb / Retroviral aspartyl protease / Retroviral matrix protein / Ribonuclease H-like superfamily / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Integrase-like, N-terminal / Retropepsins / Aspartic peptidase domain superfamily / Retropepsin-like catalytic domain / Ribonuclease H superfamily / Integrase, C-terminal domain superfamily, retroviral / Zinc finger, CCHC-type superfamily / Immunodeficiency lentiviral matrix, N-terminal / RNase H / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase connection domain / Integrase DNA binding domain profile. / Integrase catalytic domain profile. / RNase H domain profile. / Reverse transcriptase (RT) catalytic domain profile. / Zinc finger integrase-type profile. / Aspartyl protease, retroviral-type family profile. / Zinc finger CCHC-type profile. / Eukaryotic and viral aspartyl proteases active site. / Zinc knuckle / Reverse transcriptase thumb domain / Integrase Zinc binding domain / gag gene protein p24 (core nucleocapsid protein) / gag gene protein p17 (matrix protein) / Integrase DNA binding domain / Integrase core domain
Gag-Pol polyprotein
MethodSOLUTION NMR / simulated annealing
AuthorsBourbigot, S. / Ramalanjaona, N. / Salgado, G.F.J. / Mely, Y. / Roques, B.P. / Bouaziz, S. / Morellet, N.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription.
Authors: Bourbigot, S. / Ramalanjaona, N. / Boudier, C. / Salgado, G.F. / Roques, B.P. / Mely, Y. / Bouaziz, S. / Morellet, N.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 21, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 nucleocapsid protein NCp7(12-55)
B: DNA (5'-D(*DGP*DTP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DCP*DGP*DGP*DGP*DC)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4174
Polymers9,2872
Non-polymers1312
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide HIV-1 nucleocapsid protein NCp7(12-55)


Mass: 5022.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P03366*PLUS
#2: DNA chain DNA (5'-D(*DGP*DTP*DCP*DCP*DCP*DTP*DGP*DTP*DTP*DCP*DGP*DGP*DGP*DC)-3')


Mass: 4263.751 Da / Num. of mol.: 1 / Details: HIV-1 primer binding site PBS / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
12D 1H-1H NOESY
22D 1H-1H TOCSY
32D DQF-COSY

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Sample preparation

DetailsContents: 1 mM NCp7(12-55), 1 mM P(-)PBS, 3 mM ZnCl2, 30 mM sodium chloride, 0.2 mM MgCl2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMNCp7(12-55)1
1 mMP(-)PBS1
3 mMZnCl21
30 mMsodium chloride1
0.2 mMMgCl21
Sample conditionsIonic strength: 30 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR3Bruker Biospincollection
XWINNMR3Bruker Biospinprocessing
DISCOVER2.98Accelrysrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE 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 representativeSelection criteria: closest to the average
NMR ensembleConformer 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 rmsDistance rms dev: 0.028 Å / Distance rms dev error: 0.006 Å

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