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- PDB-6cyt: HIV-1 TAR loop in complex with Tat:AFF4:P-TEFb -

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Basic information

Entry
Database: PDB / ID: 6cyt
TitleHIV-1 TAR loop in complex with Tat:AFF4:P-TEFb
Components
  • AF4/FMR2 family member 4
  • Cyclin-T1
  • Cyclin-dependent kinase 9
  • Protein Tat
  • RNA (5'-R(P*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*U)-3')
KeywordsTRANSCRIPTION/RNA / RNA binding protein / HIV-1 Tat / transcription elongation / HIV-1 TAR / TRANSCRIPTION / 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 / protein serine/threonine phosphatase inhibitor activity / 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 / protein serine/threonine phosphatase inhibitor activity / 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 / symbiont-mediated suppression of host translation initiation / nucleus localization / evasion of host immune response / molecular sequestering activity / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to cytokine stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / spermatid development / RNA-binding transcription regulator activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / cyclin-dependent kinase / Formation of HIV elongation complex in the absence of HIV Tat / cyclin-dependent protein serine/threonine kinase activity / regulation of DNA repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / viral process / response to endoplasmic reticulum stress / cyclin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription elongation factor complex / molecular condensate scaffold activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / euchromatin / PKR-mediated signaling / fibrillar center / PML body / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / response to xenobiotic stimulus / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / virus-mediated perturbation of host defense response / cell division / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA-templated transcription / chromatin binding / host cell nucleus / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA 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-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
RNA / RNA (> 10) / Protein Tat / Cyclin-T1 / Protein Tat / Cyclin-dependent kinase 9 / AF4/FMR2 family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSchulze Gahmen, U. / Hurley, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM0882250 United States
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex.
Authors: Schulze-Gahmen, U. / Hurley, J.H.
#1: Journal: 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
DepositionApr 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3647
Polymers86,2335
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.580, 148.580, 104.630
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: 38226.309 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 aff. frugiperda 2 RZ-2014 (butterflies/moths)
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 aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: O60563
#4: Protein Protein Tat


Mass: 6784.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: tat
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: A0A0C5HAL9, UniProt: P04608*PLUS

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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: 4164.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFF4, AF5Q31, MCEF, HSPC092 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB7
#5: RNA chain RNA (5'-R(P*AP*UP*CP*UP*GP*AP*GP*CP*CP*UP*GP*GP*GP*AP*GP*CP*U)-3')


Mass: 6438.879 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: 4.13 Å3/Da / Density % sol: 70.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50 mM Tris 8.5, 0.2M Ammonium Acetate, 6 mM MgCl2, 8% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 11, 2017
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 3.5→140 Å / Num. obs: 17145 / % possible obs: 99.47 % / Redundancy: 37.6 % / CC1/2: 0.999 / Net I/σ(I): 11.1
Reflection shellResolution: 3.5→3.625 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 0.63 / Num. unique obs: 1690 / CC1/2: 0.441 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L1Z

5l1z


Resolution: 3.5→128.674 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.31
RfactorNum. reflection% reflection
Rfree0.2829 1701 9.97 %
Rwork0.2475 --
obs0.251 17060 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 329.53 Å2 / Biso mean: 154.237 Å2 / Biso min: 82.62 Å2
Refinement stepCycle: final / Resolution: 3.5→128.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 364 2 0 5621
Biso mean--178.72 --
Num. residues----671
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5002-3.60320.40171260.3831209133595
3.6032-3.71950.33871450.334812811426100
3.7195-3.85240.37411350.318812461381100
3.8524-4.00670.30161320.286112801412100
4.0067-4.18910.29731490.268812751424100
4.1891-4.40990.29581400.245712671407100
4.4099-4.68620.24261400.238612761416100
4.6862-5.04810.27371460.243112931439100
5.0481-5.55610.29291460.24812721418100
5.5561-6.360.32451420.29212931435100
6.36-8.01280.30051420.263913121454100
8.0128-128.7610.23581580.18761355151399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.81881.42516.53552.23490.7825.5342-3.1147-1.14581.7561-3.20141.70051.6776-0.4463-0.10570.99972.4514-0.06290.39662.3514-0.36713.341415.565630.084448.868
26.9793-1.93136.9321.2464-2.46777.1242-0.3332-2.16591.5786-0.11960.74311.65261.3665-2.1605-0.70951.7938-0.75990.00813.14190.18172.210217.044320.403932.5205
32.34091.5507-0.85742.4831.78094.0986-0.10582.8979-3.03130.16250.12322.9087-0.5914-1.87490.24562.5313-0.450.46623.6917-0.4742.60212.265821.685140.9875
48.90660.5972-1.5477.8488-3.51924.9712-0.1459-0.49320.4684-0.26490.5130.2638-0.9608-0.8207-0.4061.2946-0.0453-0.07811.5209-0.17990.962262.901550.887328.3972
58.29261.3508-2.95773.2989-2.36537.55340.1698-0.34520.19110.2107-0.1547-0.27930.22740.41010.00580.75470.0343-0.01140.7566-0.07440.642863.438551.237111.7608
62.24381.3796-0.79682.28690.01924.40170.8007-1.1752-1.48091.193-1.5984-0.0776-0.15680.77360.99322.096-0.24670.08692.18410.27451.849952.994423.542530.2813
75.65461.7779-0.04747.15241.62666.7042-0.1911-0.57240.0671-0.0231-0.12820.80450.4636-1.3070.37740.923-0.2250.08651.404-0.02040.816938.922533.528122.1731
83.47393.42773.41523.50373.45513.37930.29181.2891-2.7588-0.9451-0.323-0.25363.1265-1.59650.43192.7163-0.24190.14281.6822-0.54221.812344.590312.57161.3639
94.5264-4.0818-1.37334.13692.4625.2883-1.1598-0.5451-2.07040.92820.42010.5992.2113-0.07210.78412.1307-0.06550.19441.22780.12441.921342.519511.894718.5031
104.859-3.97291.59493.60610.24917.2849-0.49671.05281.0767-1.32242.7703-1.61640.80210.2971-2.04822.2206-1.5430.21183.3404-0.25162.07921.923212.895822.4619
116.73662.35781.03542.28153.02727.91181.6262-1.7469-2.40880.59670.2912-1.43360.99540.6955-2.63722.0778-0.79820.30051.8777-0.26972.463315.289515.171717.207
125.69965.2958-3.32328.5837-2.6891.9686-0.0479-0.6615-2.35870.8729-1.9518-0.04382.5142-4.99691.81651.876-0.95640.36742.2818-0.52291.746738.857312.1216-4.6727
137.94181.38366.3862.03381.68257.8203-0.0319-1.23121.0218-0.0154-2.6543-4.1231-1.4163-0.19792.0911.4292-0.3034-0.07931.6029-0.06693.239634.70061.75817.9577
144.52272.1279-3.86022.3459-0.86084.8901-0.92580.0505-1.8410.1868-0.0875-0.21760.9937-0.31521.34122.5406-0.68990.05542.0408-0.26352.307427.031411.039111.06
154.3761-3.1376-1.18846.7376-0.57576.99970.0397-0.0366-1.2417-1.6-0.54280.939-0.3049-0.40930.37591.493-0.2097-0.32112.0234-0.12731.299329.61732.587610.233
161.34831.43072.01583.20981.89513.0563-1.33490.8316-0.79530.20580.5227-0.3151-0.4861.2270.63591.4725-0.19020.20772.27830.06891.917826.08425.531820.9256
174.36531.87372.06154.7747-3.09475.01530.4567-0.9743-3.2319-0.6243-1.9148-0.44342.6465-4.04551.4832.7044-0.262-0.53932.4825-0.4875.420438.979644.2998-5.0275
188.7167-0.11780.38948.021-0.56079.33330.18330.7731.0196-0.5957-0.3386-0.3081-0.8851-0.11640.15471.01080.07120.09511.0390.20420.82659.270462.67-4.4542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'N' and (resid 22 through 26 )N22 - 26
2X-RAY DIFFRACTION2chain 'N' and (resid 27 through 34 )N27 - 34
3X-RAY DIFFRACTION3chain 'N' and (resid 35 through 38 )N35 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 8 through 55 )A8 - 55
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 177 )A56 - 177
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 27 )B7 - 27
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 205 )B28 - 205
8X-RAY DIFFRACTION8chain 'B' and (resid 206 through 226 )B206 - 226
9X-RAY DIFFRACTION9chain 'B' and (resid 227 through 250 )B227 - 250
10X-RAY DIFFRACTION10chain 'B' and (resid 251 through 254 )B251 - 254
11X-RAY DIFFRACTION11chain 'B' and (resid 255 through 261 )B255 - 261
12X-RAY DIFFRACTION12chain 'C' and (resid 34 through 41 )C34 - 41
13X-RAY DIFFRACTION13chain 'C' and (resid 42 through 48 )C42 - 48
14X-RAY DIFFRACTION14chain 'C' and (resid 49 through 64 )C49 - 64
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 30 )D1 - 30
16X-RAY DIFFRACTION16chain D and (resid 31 through 48)D31 - 48
17X-RAY DIFFRACTION17chain 'A' and (resid 178 through 181 )A178 - 181
18X-RAY DIFFRACTION18chain 'A' and (resid 182 through 330 )A182 - 330

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