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- PDB-4or5: Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4 -

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Basic information

Entry
Database: PDB / ID: 4or5
TitleCrystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4
Components
  • AF4/FMR2 family member 4
  • Cyclin-T1
  • Cyclin-dependent kinase 9
  • Protein Tat
KeywordsTransferase/Transcription / Cdk9 / Tat / AFF4 / Zinc Finger / Transcription / RNA binding / Phosphorylation / Transferase-Transcription 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 / protein serine/threonine phosphatase inhibitor activity / 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 / protein serine/threonine phosphatase inhibitor activity / 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 / symbiont-mediated suppression of host translation initiation / molecular sequestering activity / evasion of host immune response / nucleus localization / host cell nucleolus / actinin binding / cyclin-dependent protein serine/threonine kinase activator activity / positive regulation by host of viral transcription / transcription elongation-coupled chromatin remodeling / RNA polymerase binding / negative regulation of protein localization to chromatin / [RNA-polymerase]-subunit kinase / positive regulation of DNA-templated transcription, elongation / replication fork processing / negative regulation of peptidyl-threonine phosphorylation / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to cytokine stimulus / spermatid development / 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 / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA-binding transcription regulator activity / Formation of HIV elongation complex in the absence of HIV Tat / regulation of DNA repair / cyclin-dependent kinase / 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 / transcription elongation factor complex / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / 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 / PML body / fibrillar center / cytoplasmic ribonucleoprotein granule / transcription coactivator binding / kinase activity / regulation of gene expression / cell population proliferation / Estrogen-dependent gene expression / host cell cytoplasm / DNA-binding transcription factor binding / 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 / protein domain specific binding / cell division / 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 / host cell nucleus / 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-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
YTTRIUM (III) ION / Cyclin-T1 / Protein Tat / Cyclin-dependent kinase 9 / AF4/FMR2 family member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGu, J. / Babayeva, N.D. / Suwa, Y. / Baranovskiy, A.G. / Price, D.H. / Tahirov, T.H.
CitationJournal: Cell Cycle / Year: 2014
Title: Crystal structure of HIV-1 Tat complexed with human P-TEFb and AFF4.
Authors: Gu, J. / Babayeva, N.D. / Suwa, Y. / Baranovskiy, A.G. / Price, D.H. / Tahirov, T.H.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references

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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: Protein Tat
E: AF4/FMR2 family member 4
F: Cyclin-dependent kinase 9
G: Cyclin-T1
H: Protein Tat
J: AF4/FMR2 family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,54432
Polymers157,4768
Non-polymers2,06824
Water1,802100
1
A: Cyclin-dependent kinase 9
B: Cyclin-T1
C: Protein Tat
E: AF4/FMR2 family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,77216
Polymers78,7384
Non-polymers1,03412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-194 kcal/mol
Surface area30940 Å2
MethodPISA
2
F: Cyclin-dependent kinase 9
G: Cyclin-T1
H: Protein Tat
J: AF4/FMR2 family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,77216
Polymers78,7384
Non-polymers1,03412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-199 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.862, 186.739, 108.661
Angle α, β, γ (deg.)90.00, 120.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-519-

HOH

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Components

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Protein , 2 types, 4 molecules AFBG

#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: 37544.574 Da / Num. of mol.: 2 / Fragment: UNP residues 7-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK9, CDC2L4, TAK
References: UniProt: P50750, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein Cyclin-T1 / CycT1 / Cyclin-T


Mass: 30877.320 Da / Num. of mol.: 2 / Fragment: UNP residues 1-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNT1 / References: UniProt: O60563

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Protein/peptide , 2 types, 4 molecules CHEJ

#3: Protein/peptide Protein Tat / Transactivating regulatory protein


Mass: 5428.422 Da / Num. of mol.: 2 / Fragment: UNP residues 1-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 (virus) / Strain: isolate HXB2 / Gene: tat / References: UniProt: P04608
#4: 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: 4887.460 Da / Num. of mol.: 2 / Fragment: UNP residues 32-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AFF4, AF5Q31, MCEF, HSPC092 / References: UniProt: Q9UHB7

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Non-polymers , 4 types, 124 molecules

#5: Chemical
ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Y
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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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: 4.64 Å3/Da / Density % sol: 73.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM MES pH6.5, 3.7-3.75% w/v PEG 20000, 5 mM YCl3, 200 mM NDSB 211, 2 mM TCEP pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 67551 / Num. obs: 67551 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.2 / % possible all: 87.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→41.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5136435.76 / 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
Rfree0.267 3092 5.1 %RANDOM
Rwork0.225 ---
obs0.225 60890 95.8 %-
all-60890 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.6498 Å2 / ksol: 0.312516 e/Å3
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å212.99 Å2
2---1.23 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.92 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 2.9→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10755 0 40 100 10895
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.741.5
X-RAY DIFFRACTIONc_mcangle_it6.022
X-RAY DIFFRACTIONc_scbond_it5.012
X-RAY DIFFRACTIONc_scangle_it7.312.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 478 5.1 %
Rwork0.422 8981 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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