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- PDB-9de5: Structure of full-length HIV TAR RNA bound to HIV Tat RNA-binding... -

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Basic information

Entry
Database: PDB / ID: 9de5
TitleStructure of full-length HIV TAR RNA bound to HIV Tat RNA-binding domain
Components
  • Protein Tat
  • RNA (55-MER)
KeywordsRNA/TRANSCRIPTION / viral RNA / HIV RNA / TAR RNA / RNA-protein complex / HIV tat / RNA binding protein / RNA / RNA-TRANSCRIPTION complex
Function / homology
Function and homology information


trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / symbiont-mediated perturbation of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / : / RNA-binding transcription regulator activity / cyclin binding ...trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / symbiont-mediated perturbation of host chromatin organization / symbiont-mediated suppression of host translation initiation / host cell nucleolus / actinin binding / : / RNA-binding transcription regulator activity / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein domain specific binding / DNA-templated transcription / extracellular region / metal ion binding
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat)
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / Protein Tat
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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

Downloads & links

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Assembly

Deposited unit
C: RNA (55-MER)
E: RNA (55-MER)
B: RNA (55-MER)
D: RNA (55-MER)
A: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1198
Polymers76,0025
Non-polymers1173
Water1629
1
B: RNA (55-MER)
A: Protein Tat


Theoretical massNumber of molelcules
Total (without water)20,6222
Polymers20,6222
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4601
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: RNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4601
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (55-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4992
Polymers18,4601
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.872, 40.515, 120.406
Angle α, β, γ (deg.)90.000, 94.606, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: RNA chain
RNA (55-MER)


Mass: 18459.848 Da / Num. of mol.: 4 / Mutation: U31G, G32A / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: GenBank: 1945658931
#2: Protein/peptide Protein Tat / Transactivating regulatory protein


Mass: 2162.533 Da / Num. of mol.: 1 / Fragment: residues 44-60 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05907
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: Apr 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.749→47.093 Å / Num. obs: 17526 / % possible obs: 97.84 % / Redundancy: 7.4 % / CC1/2: 0.994 / Net I/σ(I): 4.89
Reflection shellResolution: 2.749→2.847 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 1742 / CC1/2: 0.711

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→47.09 Å / SU ML: 0.4331 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.6417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2879 829 4.78 %
Rwork0.2485 16520 -
obs0.2504 17349 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.21 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 4756 3 9 4902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185439
X-RAY DIFFRACTIONf_angle_d0.55668431
X-RAY DIFFRACTIONf_chiral_restr0.02431120
X-RAY DIFFRACTIONf_plane_restr0.0037244
X-RAY DIFFRACTIONf_dihedral_angle_d22.38283274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.920.43611460.3922728X-RAY DIFFRACTION98.86
2.92-3.150.41761320.34492704X-RAY DIFFRACTION97.32
3.15-3.460.34091500.28132679X-RAY DIFFRACTION96.52
3.46-3.960.27711290.23412711X-RAY DIFFRACTION96.63
3.96-4.990.2511340.20962841X-RAY DIFFRACTION99.56
4.99-47.090.20481380.20072857X-RAY DIFFRACTION98.04

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