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- PDB-3mia: Crystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb -

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Basic information

Entry
Database: PDB / ID: 3mia
TitleCrystal structure of HIV-1 Tat complexed with ATP-bound human P-TEFb
Components
  • Cell division protein kinase 9
  • Cyclin-T1
  • Protein Tat
KeywordsPROTEIN BINDING / P-TEFb / Cdk9 / Cyclin T1 / HIV-1 / Tat
Function / homology
Function and homology information


symbiont-mediated suppression of host antigen processing and presentation / trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / nucleus localization / protein serine/threonine phosphatase inhibitor activity / 7SK snRNA binding / RNA polymerase core enzyme binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex ...symbiont-mediated suppression of host antigen processing and presentation / trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / nucleus localization / protein serine/threonine phosphatase inhibitor activity / 7SK snRNA binding / RNA polymerase core enzyme binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / regulation of muscle cell differentiation / symbiont-mediated perturbation of host chromatin organization / symbiont-mediated suppression of host translation initiation / symbiont-mediated evasion of host immune response / negative regulation of peptidyl-threonine phosphorylation / host cell nucleolus / transcription regulator activator activity / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation factor activity / host-mediated activation of viral transcription / cyclin-dependent protein serine/threonine kinase activator activity / RNA polymerase binding / actinin binding / positive regulation of DNA-templated transcription, elongation / [RNA-polymerase]-subunit kinase / transcription elongation-coupled chromatin remodeling / histone acetyltransferase binding / cellular response to cytokine stimulus / replication fork processing / molecular sequestering activity / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Tat-mediated elongation of the HIV-1 transcript / RNA-binding transcription regulator activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / regulation of DNA repair / Formation of HIV elongation complex in the absence of HIV Tat / nucleosome binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of protein localization to chromatin / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / transcription elongation factor complex / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / molecular condensate scaffold activity / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PKR-mediated signaling / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / kinase activity / Estrogen-dependent gene expression / DNA-binding transcription factor binding / transcription by RNA polymerase II / host cell cytoplasm / protein phosphorylation / protein kinase activity / cell population proliferation / transcription cis-regulatory region binding / regulation of cell cycle / symbiont-mediated suppression of host innate immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / response to xenobiotic stimulus / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / chromatin binding / DNA-templated transcription / protein kinase binding / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / ATP binding / metal ion binding / membrane / nucleus / cytosol
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain ...Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cyclin-T1 / Protein Tat / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsTahirov, T.H. / Babayeva, N.D. / Varzavand, K. / Cooper, J.J. / Sedore, S.C. / Price, D.H.
CitationJournal: Nature / Year: 2010
Title: Crystal structure of HIV-1 Tat complexed with human P-TEFb.
Authors: Tahirov, T.H. / Babayeva, N.D. / Varzavand, K. / Cooper, J.J. / Sedore, S.C. / Price, D.H.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 9
B: Cyclin-T1
C: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0797
Polymers81,4183
Non-polymers6614
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-85 kcal/mol
Surface area29510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.286, 134.286, 97.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Cell division protein kinase 9 / Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / Cell division cycle 2-like ...Cyclin-dependent kinase 9 / Serine/threonine-protein kinase PITALRE / Cell division cycle 2-like protein kinase 4 / C-2K


Mass: 40692.152 Da / Num. of mol.: 1 / Fragment: UNP residues 1-345, Protein kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC2L4, CDK9 / Plasmid: pENTR/SD/D-TOPO vector (Invitrogen K2420) / Cell (production host): insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / Cyclin-T / CycT1


Mass: 30877.320 Da / Num. of mol.: 1 / Fragment: UNP residues 1-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1, Cyclin T1 / Plasmid: pENTR/SD/D-TOPO vector (Invitrogen K2420) / Cell (production host): insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O60563
#3: Protein Protein Tat / Transactivating regulatory protein


Mass: 9848.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: isolate HXB2 group M subtype B / Gene: tat / Plasmid: pENTR/SD/D-TOPO vector (Invitrogen K2420) / Cell (production host): insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P04608

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Non-polymers , 4 types, 31 molecules

#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES buffer (pH 7.5), 4.25-5% PEG 20,000, 1 mM TCEP, and 20 mM glycyl-glycyl-glycine. The Tat P-TEFb ATP crystals were obtained by soaking the Tat P-TEFb crystals in crystallization ...Details: 50 mM HEPES buffer (pH 7.5), 4.25-5% PEG 20,000, 1 mM TCEP, and 20 mM glycyl-glycyl-glycine. The Tat P-TEFb ATP crystals were obtained by soaking the Tat P-TEFb crystals in crystallization solution with 1mM ATP analog AMPPNP and 5 mM magnesium chloride for 40 min., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 19980 / % possible obs: 96.9 % / Observed criterion σ(I): -2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 30.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.7 / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3mi9

3mi9


Resolution: 3→30.61 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2849681.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 933 4.9 %RANDOM
Rwork0.219 ---
obs0.219 19001 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.7012 Å2 / ksol: 0.328984 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å29.36 Å20 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 34 27 5069
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.662
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.932.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 158 5.5 %
Rwork0.297 2737 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater
X-RAY DIFFRACTION4ion.paramion
X-RAY DIFFRACTION5ANP.parANP.top

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