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- PDB-2ou2: Acetyltransferase domain of Human HIV-1 Tat interacting protein, ... -

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Basic information

Entry
Database: PDB / ID: 2ou2
TitleAcetyltransferase domain of Human HIV-1 Tat interacting protein, 60kDa, isoform 3
ComponentsHistone acetyltransferase HTATIP
KeywordsTRANSFERASE / Histone acetyltransferase HTATIP / TIP / TIP60 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H2AK5 acetyltransferase activity / peptide crotonyltransferase activity / histone H2A acetyltransferase activity / positive regulation of mitotic sister chromatid segregation / positive regulation of protein acetylation / piccolo histone acetyltransferase complex / Sensing of DNA Double Strand Breaks / MSL complex / peptide butyryltransferase activity / lipid droplet disassembly ...histone H2AK5 acetyltransferase activity / peptide crotonyltransferase activity / histone H2A acetyltransferase activity / positive regulation of mitotic sister chromatid segregation / positive regulation of protein acetylation / piccolo histone acetyltransferase complex / Sensing of DNA Double Strand Breaks / MSL complex / peptide butyryltransferase activity / lipid droplet disassembly / histone H4K16 acetyltransferase activity / sperm DNA condensation / peptide 2-hydroxyisobutyryltransferase activity / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Swr1 complex / positive regulation of triglyceride biosynthetic process / peptidyl-lysine acetylation / histone H4 acetyltransferase activity / regulation of double-strand break repair / Impaired BRCA2 binding to PALB2 / positive regulation of regulatory T cell differentiation / positive regulation of circadian rhythm / positive regulation of innate immune response / DNA repair-dependent chromatin remodeling / Cardiogenesis / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / neural tube development / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / regulation of hematopoietic stem cell differentiation / Resolution of D-loop Structures through Holliday Junction Intermediates / NuA4 histone acetyltransferase complex / negative regulation of interleukin-2 production / HDR through Single Strand Annealing (SSA) / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Impaired BRCA2 binding to RAD51 / peptide-lysine-N-acetyltransferase activity / negative regulation of double-strand break repair via homologous recombination / response to ionizing radiation / positive regulation of double-strand break repair via homologous recombination / mitotic spindle pole / spermatid development / establishment of mitotic spindle orientation / acetyltransferase activity / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of myoblast differentiation / cellular response to glucose starvation / positive regulation of autophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / cellular response to estradiol stimulus / nucleotide-excision repair / cellular response to glucose stimulus / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / kinetochore / double-strand break repair / nucleosome / cellular senescence / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / HATs acetylate histones / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / transcription coactivator activity / regulation of cell cycle / innate immune response / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
N-acetyl transferase-like / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain ...N-acetyl transferase-like / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase KAT5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMin, J. / Wu, H. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of acetyltransferase domain of Human HIV-1 Tat interacting protein in complex with acetylcoenzyme A.
Authors: Wu, H. / Min, J. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase HTATIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8153
Polymers32,9401
Non-polymers8752
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.632, 107.632, 133.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Histone acetyltransferase HTATIP / 60 kDa Tat interactive protein / Tip60 / HIV-1 Tat interactive protein / cPLA(2)-interacting protein


Mass: 32940.055 Da / Num. of mol.: 1 / Fragment: Acetyltransferase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTATIP, TIP60 / Plasmid: Pet28a_MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92993, histone acetyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Purified HTATIP was complexed with acetylcoenzyme A (AcCoA) (Sigma) at 1:10 molar ratio of protein:AcCoA and crystallized using the hanging drop vapor diffusion method at 20 deg C by mixing ...Details: Purified HTATIP was complexed with acetylcoenzyme A (AcCoA) (Sigma) at 1:10 molar ratio of protein:AcCoA and crystallized using the hanging drop vapor diffusion method at 20 deg C by mixing 1 microliter of the protein solution with 1 microliter of the reservoir solution containing 16% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.6., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2006
RadiationMonochromator: si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→83.92 Å / Num. all: 17598 / Num. obs: 17598 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GIV

2giv


Resolution: 2.3→83.92 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.075 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25215 893 5.1 %RANDOM
Rwork0.21983 ---
obs0.22145 16701 98.77 %-
all-16701 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.3→83.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 52 30 2128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222150
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4552.0142908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37723.47495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8351511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021575
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2862
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.51272
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41821998
X-RAY DIFFRACTIONr_scbond_it1.97331025
X-RAY DIFFRACTIONr_scangle_it3.0554.5910
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 66 -
Rwork0.277 1210 -
obs--99.22 %

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