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- PDB-9de8: Structure of full-length HIV TAR RNA soaked in CaCl2 -

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Basic information

Entry
Database: PDB / ID: 9de8
TitleStructure of full-length HIV TAR RNA soaked in CaCl2
ComponentsRNA (56-MER)
KeywordsRNA / viral RNA / HIV RNA / TAR RNA / Ca2+ / Calcium / bulge
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.76 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 (56-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3402
Polymers18,3001
Non-polymers401
Water1267
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)31.588, 47.266, 132.729
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)

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Components

#1: RNA chain RNA (56-MER)


Mass: 18299.889 Da / Num. of mol.: 1 / Mutation: G16A, A17G, U31G, G32A / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 1945658931
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
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). Soaking with 100 mM CaCl2 for 2 hours at 20 degrees Celsius

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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: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→44.53 Å / Num. obs: 5512 / % possible obs: 99.17 % / Redundancy: 42.8 % / CC1/2: 0.999 / Net I/σ(I): 13.82
Reflection shellResolution: 2.761→2.86 Å / Mean I/σ(I) obs: 1.62 / Num. unique obs: 529 / CC1/2: 0.669

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.76→44.53 Å / SU ML: 0.2966 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8864
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: A separate dataset of lower quality, which was not deposited, was used for SAD phasing.
RfactorNum. reflection% reflection
Rfree0.2951 266 4.84 %
Rwork0.2455 5231 -
obs0.2477 5497 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.04 Å2
Refinement stepCycle: LAST / Resolution: 2.76→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1174 1 7 1182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00171311
X-RAY DIFFRACTIONf_angle_d0.4242040
X-RAY DIFFRACTIONf_chiral_restr0.019278
X-RAY DIFFRACTIONf_plane_restr0.002554
X-RAY DIFFRACTIONf_dihedral_angle_d21.5495807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-3.480.40731190.3322545X-RAY DIFFRACTION98.85
3.48-44.530.2621470.21652686X-RAY DIFFRACTION99.54

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