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- PDB-3mi9: Crystal structure of HIV-1 Tat complexed with human P-TEFb -

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Basic information

Entry
Database: PDB / ID: 3mi9
TitleCrystal structure of HIV-1 Tat complexed with human P-TEFb
Components
  • Cell division protein kinase 9
  • Cyclin-T1
  • Protein Tat
KeywordsPROTEIN BINDING / P-TEFb / Tat / HIV-1
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 / negative regulation of protein localization to chromatin / 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 / 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 / cell population proliferation / protein kinase activity / 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 / DNA-templated transcription / chromatin binding / protein kinase binding / host cell nucleus / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular region / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / 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
Cyclin-T1 / Protein Tat / Cyclin-dependent kinase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Nov 27, 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)81,5495
Polymers81,4183
Non-polymers1312
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-72 kcal/mol
Surface area30370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.306, 132.306, 95.358
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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 line (production host): BL21 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 line (production host): BL21 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 line (production host): BL21 insect cells / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P04608
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.43 %
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 , VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 51839 / % possible obs: 90.9 % / Observed criterion σ(F): -2 / Redundancy: 2.5 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 35
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.7 / Num. unique all: 2531 / % possible all: 89

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3blh

3blh


Resolution: 2.1→30.63 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2384386.28 / 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
Rfree0.264 2443 5.1 %RANDOM
Rwork0.219 ---
obs0.219 48306 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0275 Å2 / ksol: 0.36834 e/Å3
Displacement parametersBiso mean: 46.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å21.87 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 2 341 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.541.5
X-RAY DIFFRACTIONc_mcangle_it5.82
X-RAY DIFFRACTIONc_scbond_it6.682
X-RAY DIFFRACTIONc_scangle_it7.852.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 355 4.9 %
Rwork0.356 6931 -
obs--78.2 %
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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