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- PDB-5i1r: Quantitative characterization of configurational space sampled by... -

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Basic information

Entry
Database: PDB / ID: 5i1r
TitleQuantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR and X-ray scattering
ComponentsNucleocapsid protein p7
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex ...host cellular component / Synthesis And Processing Of GAG, GAGPOL Polyproteins / host cell nuclear membrane / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / viral budding via host ESCRT complex / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / Budding and maturation of HIV virion / host multivesicular body / viral nucleocapsid / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 1
MethodSOLUTION NMR / SOLUTION SCATTERING / simulated annealing
AuthorsDeshmukh, L. / Schwieters, C.D. / Grishaev, A. / Clore, G.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: Chemphyschem / Year: 2016
Title: Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.
Authors: Deshmukh, L. / Schwieters, C.D. / Grishaev, A. / Clore, G.M.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein p7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5733
Polymers6,4431
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #alllowest energy

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Components

#1: Protein Nucleocapsid protein p7 / Pr55Gag


Mass: 6442.522 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: zinc atoms
Source: (gene. exp.) Human immunodeficiency virus type 1 (HXB2 ISOLATE)
Strain: isolate HXB2 / Gene: gag / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P04591
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn / Details: zinc atoms

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HNCA
141isotropic13D HN(CA)CB
152anisotropic22D ARTSY
162anisotropic13D Quntitaive HNCO - NC'
172anisotropic13D Quntitaive HNCO - CaC'

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 93% H2O/7% D2OCDN_Sample93% H2O/7% D2O
bicelle20.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 5 % neutral bicelles, 93% H2O/7% D2OCDN_Sample_193% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMNucleocapsid protein of human immunodeficiency virus 1 (HIV-1)[U-13C; U-15N; U-2H]1
50 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
1 mMDithiothreitolnatural abundance1
0.1 mMzinc chloridenatural abundance1
0.2 mMNucleocapsid protein of human immunodeficiency virus 1 (HIV-1)[U-13C; U-15N; U-2H]2
50 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
1 mMDithiothreitolnatural abundance2
0.1 mMzinc chloridenatural abundance2
5 %neutral bicellesnatural abundance2
Sample conditionsIonic strength: 50 mM / Label: Buffer_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.41C. D. Schwieters, J. J. Kuszewski, N. Tjandra, G. M. Clorerefinement
Analysis2.2.2W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon, M. Llinas, E. L. Ulrich, J. L. Markley, J. Ionides, E. D. Lauechemical shift assignment
Analysis2.2.2W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon, M. Llinas, E. L. Ulrich, J. L. Markley, J. Ionides, E. D. Lauepeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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