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- PDB-9de6: Structure of full-length HIV TAR RNA -

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Basic information

Entry
Database: PDB / ID: 9de6
TitleStructure of full-length HIV TAR RNA
ComponentsRNA (57-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 / MOLECULAR REPLACEMENT / Resolution: 2.35 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 (57-MER)
B: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9684
Polymers36,9202
Non-polymers492
Water1086
1
A: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4842
Polymers18,4601
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (57-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4842
Polymers18,4601
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.253, 41.982, 68.570
Angle α, β, γ (deg.)90.000, 93.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 23 or resid 25 through 59))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GTPGTPUU(chain A and (resid 2 through 23 or resid 25 through 59))AA2 - 231 - 22
12UUMGMG(chain A and (resid 2 through 23 or resid 25 through 59))AA - C25 - 10124
21GTPGTPHOHHOHchain BBB - F2 - 2031

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Components

#1: RNA chain RNA (57-MER)


Mass: 18459.848 Da / Num. of mol.: 2 / Mutation: U31G, G32A / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 1945658931
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 12 mM NaCl, 80 mM KCl, 50 mM sodium cacodylate pH 5.5, 2 mM hexamine cobalt and 45% v/v 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: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→35.79 Å / Num. obs: 17435 / % possible obs: 97.46 % / Redundancy: 6.6 % / Biso Wilson estimate: 69.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.38
Reflection shellResolution: 2.35→2.434 Å / Mean I/σ(I) obs: 1.63 / Num. unique obs: 8976 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→35.79 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 48.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2825 734 5.1 %
Rwork0.2643 13671 -
obs0.2652 14405 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.96 Å2 / Biso mean: 100.1941 Å2 / Biso min: 71.01 Å2
Refinement stepCycle: final / Resolution: 2.35→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2384 2 6 2392
Biso mean--92.18 88.72 -
Num. residues----113
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1350X-RAY DIFFRACTION10.746TORSIONAL
12B1350X-RAY DIFFRACTION10.746TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.530.46961270.49292698282597
2.53-2.780.58491150.4972776289198
2.78-3.190.39041610.39122670283196
3.19-4.010.26891650.28022650281595
4.01-35.790.23381660.195328773043100
Refinement TLS params.Method: refined / Origin x: -5.7105 Å / Origin y: -6.6556 Å / Origin z: -22.0854 Å
111213212223313233
T0.6369 Å20.0001 Å20.328 Å2-0.7324 Å20.0392 Å2--0.8986 Å2
L0.1054 °2-0.6058 °2-1.711 °2-0.11 °20.8652 °2--2.485 °2
S-0.0762 Å °-0.366 Å °-0.0109 Å °-0.0271 Å °0.0576 Å °0.0217 Å °0.011 Å °0.3098 Å °0.0912 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 62
2X-RAY DIFFRACTION1allB2 - 62

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