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- PDB-5l1z: TAR complex with HIV-1 Tat-AFF4-P-TEFb -

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Basic information

Entry
Database: PDB / ID: 5l1z
TitleTAR complex with HIV-1 Tat-AFF4-P-TEFb
Components
  • AF4/FMR2 family member 4
  • Cyclin-T1
  • Cyclin-dependent kinase 9
  • Protein Tat
  • RNA (5'-R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*U)-3')
Keywordstranscription/RNA / HIV-1 TAR / protein-RNA complex / transcription / protein kinase / transcription-RNA complex
Function / homology
Function and homology information


: / super elongation complex / trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing ...: / super elongation complex / trans-activation response element binding / P-TEFb complex / Interactions of Tat with host cellular proteins / 7SK snRNA binding / positive regulation of viral transcription / cyclin/CDK positive transcription elongation factor complex / regulation of muscle cell differentiation / regulation of mRNA 3'-end processing / positive regulation of protein localization to chromatin / modulation by virus of host chromatin organization / nucleus localization / host cell nucleolus / actinin binding / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / RNA polymerase binding / positive regulation of DNA-templated transcription, elongation / negative regulation of protein localization to chromatin / [RNA-polymerase]-subunit kinase / transcription elongation-coupled chromatin remodeling / replication fork processing / negative regulation of peptidyl-threonine phosphorylation / cellular response to cytokine stimulus / regulation of cyclin-dependent protein serine/threonine kinase activity / spermatid development / 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 / RNA-binding transcription regulator activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / regulation of DNA repair / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / molecular condensate scaffold activity / response to endoplasmic reticulum stress / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription elongation factor complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / euchromatin / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / PML body / fibrillar center / kinase activity / regulation of gene expression / DNA-binding transcription factor binding / Estrogen-dependent gene expression / cell population proliferation / host cell cytoplasm / transcription by RNA polymerase II / transcription cis-regulatory region binding / regulation of cell cycle / protein kinase activity / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
AF-4 proto-oncoprotein N-terminal region / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF4 interaction motif / AFF4, C-terminal homology domain / Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) ...AF-4 proto-oncoprotein N-terminal region / AF4/FMR2 family / AF4 interaction motif / AF4/FMR2, C-terminal homology domain / AF4 interaction motif / AFF4, C-terminal homology domain / Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / : / Transactivating regulatory protein (Tat) / Cyclin-T2-like, C-terminal domain / Haspin like kinase domain / Cyclin/Cyclin-like subunit Ssn8 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 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
Similarity search - Domain/homology
RNA / RNA (> 10) / Cyclin-T1 / Cyclin-dependent kinase 9 / Protein Tat / AF4/FMR2 family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1 group M subtype B
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 5.9 Å
AuthorsSchulze-Gahmen, U. / Hurley, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2016
Title: Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex.
Authors: Schulze-Gahmen, U. / Echeverria, I. / Stjepanovic, G. / Bai, Y. / Lu, H. / Schneidman-Duhovny, D. / Doudna, J.A. / Zhou, Q. / Sali, A. / Hurley, J.H.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _struct_conn.conn_type_id / _struct_conn.id / _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_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_conn.ptnr2_label_seq_id
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 9
B: Cyclin-T1
C: AF4/FMR2 family member 4
D: Protein Tat
N: RNA (5'-R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0527
Polymers86,9215
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-105 kcal/mol
Surface area33330 Å2
2
A: Cyclin-dependent kinase 9
B: Cyclin-T1
C: AF4/FMR2 family member 4
D: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6966
Polymers79,5654
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-102 kcal/mol
Surface area29680 Å2
MethodPISA
3
N: RNA (5'-R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*U)-3')

N: RNA (5'-R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*U)-3')


Theoretical massNumber of molelcules
Total (without water)14,7132
Polymers14,7132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_558y,x,-z+31
Buried area1230 Å2
ΔGint-6 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.870, 146.870, 103.750
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 3 types, 3 molecules ABD

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


Mass: 38031.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9, CDC2L4, TAK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / Cyclin-T


Mass: 30618.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O60563
#4: Protein Protein Tat / Transactivating regulatory protein


Mass: 6784.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: tat / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P69697

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Protein/peptide / RNA chain / Non-polymers , 3 types, 4 molecules CN

#3: Protein/peptide AF4/FMR2 family member 4 / ALL1-fused gene from chromosome 5q31 protein / Protein AF-5q31 / Major CDK9 elongation factor- ...ALL1-fused gene from chromosome 5q31 protein / Protein AF-5q31 / Major CDK9 elongation factor-associated protein


Mass: 4130.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UHB7
#5: RNA chain RNA (5'-R(P*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*U)-3')


Mass: 7356.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.72 Å3/Da / Density % sol: 66.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: crystallized from 50 mM Tris 8.5, 0.2M AmmAcetate, 6 mM MgCl2, 8% PEG 4K at 291 degree K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 5.28→500 Å / Num. obs: 4988 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 400.752 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.258 / Rrim(I) all: 0.272 / Χ2: 1.034 / Net I/σ(I): 7.4 / Num. measured all: 48528
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. possibleNum. unique obs% possible allRmerge(I) obsRrim(I) allCC1/2
5.28-5.410.093716370370100
5.41-5.560.08322434334099.1
5.56-5.720.25327534234199.78.2368.701
5.72-5.90.3633583283281005.3175.5980.306
5.9-6.090.334003313311006.1876.5150.288
6.09-6.310.47300829729699.74.7234.9740.269
6.31-6.540.5131733163161004.1284.3520.442
6.54-6.810.7327932922921003.0333.2050.412
6.81-7.111.3726062762761001.6311.7260.842
7.11-7.462.1428922882881001.1021.1620.869
7.46-7.873.9924292412411000.5120.540.991
7.87-8.345.8224122402401000.3940.4150.979
8.34-8.929.3622092312311000.2160.2280.997
8.92-9.6313.7420362232231000.1360.1440.999
9.63-10.5520.5520342042041000.0930.0980.999
10.55-11.830.0217481821821000.0620.0661
11.8-13.6228.5413601561561000.070.0740.998
13.62-16.6833.0113251451451000.0590.0630.999
16.68-23.644.2310001151151000.040.0430.999
23.647.7753073731000.0230.0251

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CNSrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 4OGR

4ogr


Resolution: 5.9→500 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3132 347 9.6 %
Rwork0.2169 3248 -
obs-3595 100 %
Solvent computationBsol: 308.491 Å2
Displacement parametersBiso max: 696.31 Å2 / Biso mean: 424.4889 Å2 / Biso min: 245.73 Å2
Baniso -1Baniso -2Baniso -3
1-79.055 Å20 Å20 Å2
2--79.055 Å20 Å2
3----158.111 Å2
Refinement stepCycle: final / Resolution: 5.9→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 448 2 0 5716
Biso mean--585.32 --
Num. residues----671
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.806
X-RAY DIFFRACTIONc_mcbond_it16.33915
X-RAY DIFFRACTIONc_scbond_it22.14520
X-RAY DIFFRACTIONc_mcangle_it25.35820
X-RAY DIFFRACTIONc_scangle_it32.74125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
5.9-6.110.5555420.465332336599.7
6.11-6.360.4119450.4395299344100
6.36-6.640.3904200.3545326346100
6.64-70.4134360.3223316352100
7-7.430.3955380.2981316354100
7.43-8.010.3911310.2468328359100
8.01-8.810.3213290.1612321350100
8.81-10.090.2512290.1539331360100
10.09-12.710.2093340.1411339373100
12.71-500.010.304430.2199349392100
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6capping.param
X-RAY DIFFRACTION7TPOnew.param

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