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- PDB-9de7: Structure of full-length HIV TAR RNA G16A/A17G -

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Basic information

Entry
Database: PDB / ID: 9de7
TitleStructure of full-length HIV TAR RNA G16A/A17G
ComponentsRNA (58-MER)
KeywordsRNA / viral RNA / HIV RNA / TAR RNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsBou-Nader, C. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling.
Authors: Bou-Nader, C. / Link, K.A. / Suddala, K.C. / Knutson, J.R. / Zhang, J.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (58-MER)


Theoretical massNumber of molelcules
Total (without water)18,7891
Polymers18,7891
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.538, 32.580, 46.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-134-

HOH

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Components

#1: RNA chain RNA (58-MER)


Mass: 18789.053 Da / Num. of mol.: 1 / Mutation: G16A, A17G, U31G, G32A, C59A / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 1945658931
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate pH 6.5, 80 mM NaCl, 12 mM spermine and 30% v/v 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→33.135 Å / Num. obs: 70998 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.991 / Net I/σ(I): 7.98
Reflection shellResolution: 2.25→2.331 Å / Mean I/σ(I) obs: 1.57 / Num. unique obs: 7124 / CC1/2: 0.442

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→33.135 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.94 / Stereochemistry target values: ML
Details: A separate dataset of lower quality, which was not deposited, was used for SAD phasing.
RfactorNum. reflection% reflection
Rfree0.2218 1831 10.03 %
Rwork0.1933 16424 -
obs0.1962 18255 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.12 Å2 / Biso mean: 55.1072 Å2 / Biso min: 28.48 Å2
Refinement stepCycle: final / Resolution: 2.25→33.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1220 0 38 1258
Biso mean---45.18 -
Num. residues----58
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2502-2.31110.39171450.3402126999
2.3111-2.37910.32351350.315121798
2.3791-2.45580.34191470.33131297100
2.4558-2.54360.38021340.2871123299
2.5436-2.64540.32171420.28351269100
2.6454-2.76570.28391360.2829127699
2.7657-2.91140.28321440.26041263100
2.9114-3.09370.22911450.22711261100
3.0937-3.33240.22921410.18371278100
3.3324-3.66740.23081350.16691253100
3.6674-4.19710.15521490.14381269100
4.1971-5.28450.16661360.14031267100
5.2845-33.1350.18231420.15941273100
Refinement TLS params.Method: refined / Origin x: -26.1291 Å / Origin y: 10.1945 Å / Origin z: -9.3093 Å
111213212223313233
T0.2982 Å2-0.0107 Å2-0.0097 Å2-0.2624 Å2-0.0273 Å2--0.231 Å2
L2.9471 °2-2.4266 °21.5324 °2-4.6612 °2-1.8241 °2--2.218 °2
S-0.0551 Å °0.0404 Å °-0.0361 Å °0.112 Å °0.0577 Å °-0.3035 Å °-0.0578 Å °0.0941 Å °0.0047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 59
2X-RAY DIFFRACTION1allA60 - 97

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