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- PDB-2n1q: HIV-1 Core Packaging Signal -

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Basic information

Entry
Database: PDB / ID: 2n1q
TitleHIV-1 Core Packaging Signal
ComponentsRNA_(155-MER)
KeywordsRNA / HIV-1 / Packaging Signal
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
Model detailslowest energy, model13
AuthorsKeane, S.C. / Summers, M.F.
CitationJournal: Science / Year: 2015
Title: RNA structure. Structure of the HIV-1 RNA packaging signal.
Authors: Keane, S.C. / Heng, X. / Lu, K. / Kharytonchyk, S. / Ramakrishnan, V. / Carter, G. / Barton, S. / Hosic, A. / Florwick, A. / Santos, J. / Bolden, N.C. / McCowin, S. / Case, D.A. / Johnson, B. ...Authors: Keane, S.C. / Heng, X. / Lu, K. / Kharytonchyk, S. / Ramakrishnan, V. / Carter, G. / Barton, S. / Hosic, A. / Florwick, A. / Santos, J. / Bolden, N.C. / McCowin, S. / Case, D.A. / Johnson, B.A. / Salemi, M. / Telesnitsky, A. / Summers, M.F.
History
DepositionApr 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _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: RNA_(155-MER)


Theoretical massNumber of molelcules
Total (without water)50,5441
Polymers50,5441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 960structures with the lowest energy
RepresentativeModel #13lowest energy

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Components

#1: RNA chain RNA_(155-MER)


Mass: 50544.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1332D 1H-1H NOESY
1442D 1H-1H NOESY
1552D 1H-1H NOESY
1662D 1H-1H NOESY
1772D 1H-1H NOESY
1882D 1H-1H NOESY
1992D 1H-1H NOESY
110102D 1H-1H NOESY
111112D 1H-1H NOESY
112122D 1H-1H NOESY
113132D 1H-1H NOESY
114142D 1H-1H NOESY
115152D 1H-1H NOESY
116162D 1H-1H NOESY
117172D 1H-1H NOESY
118182D 1H-1H NOESY
119192D 1H-1H NOESY
120202D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1300 mM RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
2300 mM A-H, C-D, G-D, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
3300 mM A-D, C-D, G-H, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
4300 mM A-D, C-H, G-D, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
5300 mM A-D, C-D, G-D, U-5D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
6300 mM A-8D, C-D, G-8D, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
7300 mM A-8D, C,6-D2, G-D, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
8300 mM A-8D, C-D, G-D, U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
9300 mM A-8D, C,6-D2, G-8D, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
10300 mM A-8D, C-D, G-8D, U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
11300 mM A-8D, C,6-D2, G-D, U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
12300 mM A,1',2',3',4',5',5 -D7, C-D, G-D, U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
13300 mM A,1',2',3',4',5',5 -D7, C-D, G-8D, U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
14300 mM A-H, C-D, G-1',2',3',4',5',5''-D6 , U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
15300 mM A,1',2',3',4',5',5-D7, C-D, G-H, U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
16300 mM A,1',2',3',4',5',5-D7, C-D, G-D, U-H RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
17300 mM A-D, C-D, G-H, U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
18300 mM A-D, C-D, G-1',2',3',4',5',5''-D6 , U,6-D2 RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
19300 mM A-D, C-D, G-1',2',3',4',5',5''-D6 , U-5D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
20300 mM A-D, C-5D, G-1',2',3',4',5',5''-D6 , U-D RNA (155-MER), 20 mM [U-2H] TRIS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 mMRNA (155-MER)-11
20 mMTRIS-2[U-2H]1
300 mMRNA (155-MER)-3A-H, C-D, G-D, U-D2
20 mMTRIS-4[U-2H]2
300 mMRNA (155-MER)-5A-D, C-D, G-H, U-D3
20 mMTRIS-6[U-2H]3
300 mMRNA (155-MER)-7A-D, C-H, G-D, U-D4
20 mMTRIS-8[U-2H]4
300 mMRNA (155-MER)-9A-D, C-D, G-D, U-5D5
20 mMTRIS-10[U-2H]5
300 mMRNA (155-MER)-11A-8D, C-D, G-8D, U-D6
20 mMTRIS-12[U-2H]6
300 mMRNA (155-MER)-13A-8D, C-5,6-D2, G-D, U-D7
20 mMTRIS-14[U-2H]7
300 mMRNA (155-MER)-15A-8D, C-D, G-D, U-5,6-D28
20 mMTRIS-16[U-2H]8
300 mMRNA (155-MER)-17A-8D, C-5,6-D2, G-8D, U-D9
20 mMTRIS-18[U-2H]9
300 mMRNA (155-MER)-19A-8D, C-D, G-8D, U-5,6-D210
20 mMTRIS-20[U-2H]10
300 mMRNA (155-MER)-21A-8D, C-5,6-D2, G-D, U-5,6-D211
20 mMTRIS-22[U-2H]11
300 mMRNA (155-MER)-23A-8,1',2',3',4',5',5 -D7, C-D, G-D, U-5,6-D212
20 mMTRIS-24[U-2H]12
300 mMRNA (155-MER)-25A-8,1',2',3',4',5',5 -D7, C-D, G-8D, U-5,6-D213
20 mMTRIS-26[U-2H]13
300 mMRNA (155-MER)-27A-H, C-D, G-1',2',3',4',5',5''-D6 , U-D14
20 mMTRIS-28[U-2H]14
300 mMRNA (155-MER)-29A-2,1',2',3',4',5',5-D7, C-D, G-H, U-D15
20 mMTRIS-30[U-2H]15
300 mMRNA (155-MER)-31A-2,1',2',3',4',5',5-D7, C-D, G-D, U-H16
20 mMTRIS-32[U-2H]16
300 mMRNA (155-MER)-33A-D, C-D, G-H, U-5,6-D217
20 mMTRIS-34[U-2H]17
300 mMRNA (155-MER)-35A-D, C-D, G-1',2',3',4',5',5''-D6 , U-5,6-D218
20 mMTRIS-36[U-2H]18
300 mMRNA (155-MER)-37A-D, C-D, G-1',2',3',4',5',5''-D6 , U-5D19
20 mMTRIS-38[U-2H]19
300 mMRNA (155-MER)-39A-D, C-5D, G-1',2',3',4',5',5''-D6 , U-D20
20 mMTRIS-40[U-2H]20
Sample conditionsIonic strength: 20 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANArefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 960 / Conformers submitted total number: 20

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