- PDB-6mce: Solution structure of HIV-1 TAR with Tat RNA Binding Domain -
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Basic information
Entry
Database: PDB / ID: 6mce
Title
Solution structure of HIV-1 TAR with Tat RNA Binding Domain
Components
Protein Tat
TAR RNA
Keywords
TRANSCRIPTION / RNA BINDING PROTEIN
Function / homology
Function and homology information
trans-activation response element binding / Interactions of Tat with host cellular proteins / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / evasion of host immune response / molecular sequestering activity / host cell nucleolus / actinin binding ...trans-activation response element binding / Interactions of Tat with host cellular proteins / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / symbiont-mediated suppression of host translation initiation / evasion of host immune response / molecular sequestering activity / host cell nucleolus / actinin binding / negative regulation of peptidyl-threonine phosphorylation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Tat-mediated elongation of the HIV-1 transcript / RNA-binding transcription regulator activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / PKR-mediated signaling / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein domain specific binding / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / 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
Evidence: isothermal titration calorimetry, Obtain a 1:1 binding ratio in the ITC for the peptide and the RNA under the NMR conditions solved
Type
Name
Symmetry operation
Number
identity operation
1_555
1
Buried area
2050 Å2
ΔGint
-11 kcal/mol
Surface area
6660 Å2
NMR ensembles
Data
Criteria
Number of conformers (submitted / calculated)
10 / 20
structures with acceptable covalent geometry
Representative
Model #1
fewest violations
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Components
#1: RNA chain
TARRNA
Mass: 9652.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#2: Protein/peptide
ProteinTat / Transactivating regulatory protein
Mass: 2162.533 Da / Num. of mol.: 1 / Fragment: RNA Binding Domain residues 44-60 / Source method: obtained synthetically Source: (synth.) Human immunodeficiency virus type 1 group M subtype B References: UniProt: P04608
0.5 mM [U-13C; U-15N] TAR RNA, 0.5 mM Tat RNA Binding Domain, 90% H2O/10% D2O
TAR:Tat-2
90% H2O/10% D2O
solution
4
0.5 mM TAR RNA, 0.5 mM [U-13C; U-15N] Tat RNA Binding Domain selectively labeled in each of the peptides: 1) R49, K50, R57, A58 2) K51, R52, Q54,R55 3) R53, Q54, R56, 100% D2O
TAR:Tat-4
100% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.5mM
TARRNA
naturalabundance
1
0.5mM
TatRNABindingDomain
naturalabundance
1
0.5mM
TARRNA
naturalabundance
3
0.5mM
TatRNABindingDomain
naturalabundance
3
0.5mM
TARRNA
[U-13C; U-15N]
2
0.5mM
TatRNABindingDomain
naturalabundance
2
0.5mM
TARRNA
naturalabundance
4
0.5mM
TatRNABindingDomain
[U-13C; U-15N]
4
Sample conditions
Ionic strength: 10mM NaCl, 70mM NaCl, 0.1mM EDTA mM / Label: TAR Buffer / pH: 5.4 / Pressure: 100000 Pa / Temperature: 298 K
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NMR measurement
NMR spectrometer
Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz
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