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- PDB-3io2: Crystal structure of the Taz2 domain of p300 -

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Basic information

Entry
Database: PDB / ID: 3io2
TitleCrystal structure of the Taz2 domain of p300
ComponentsHistone acetyltransferase p300
KeywordsTRANSFERASE / p300 / Metal-binding / Transcription / Zinc-finger / Bromodomain / Cell cycle / Citrullination / Disease mutation / Host-virus interaction / Methylation / Nucleus / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation ...behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / regulation of tubulin deacetylation / histone H2B acetyltransferase activity / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / thigmotaxis / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / positive regulation of TORC2 signaling / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / cellular response to L-leucine / histone H3 acetyltransferase activity / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / TGFBR3 expression / positive regulation by host of viral transcription / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / face morphogenesis / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / megakaryocyte development / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / Formation of paraxial mesoderm / histone acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / PI5P Regulates TP53 Acetylation / FOXO-mediated transcription of cell death genes / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / fat cell differentiation / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / RUNX3 regulates p14-ARF / histone acetyltransferase complex / canonical NF-kappaB signal transduction / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of gluconeogenesis / NF-kappaB binding / cellular response to nutrient levels / somitogenesis / negative regulation of protein-containing complex assembly / pre-mRNA intronic binding / Attenuation phase / positive regulation of T-helper 17 cell lineage commitment / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / skeletal muscle tissue development / regulation of cellular response to heat
Similarity search - Function
CREB-binding Protein; Chain A / TAZ domain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP ...CREB-binding Protein; Chain A / TAZ domain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMiller, M. / Dauter, Z. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the Taz2 domain of p300: insights into ligand binding.
Authors: Miller, M. / Dauter, Z. / Cherry, S. / Tropea, J.E. / Wlodawer, A.
History
DepositionAug 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3May 27, 2015Group: Refinement description
Revision 1.4Jul 13, 2016Group: Refinement description
Revision 1.5Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.6Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5698
Polymers12,9881
Non-polymers5807
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.270, 155.270, 155.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300


Mass: 12988.379 Da / Num. of mol.: 1 / Fragment: residues 1723-1836 / Mutation: C1738A, C1746A, C1789A, C1790A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: CodonPlus (DE3)-RIL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q09472, histone acetyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 6.004325 Å3/Da / Density % sol: 79.514763 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.3
Details: Protein solution: 30 mg/ml Taz2, 25 mM MES pH 6.3, 100 mM NaCl, 6% glycerol, 10% TCEP. Precipitating solution: 3.2 M AMS in MES buffer pH 6.0, 10 % ethylene glycol. Both solutions mixed 1:1 ...Details: Protein solution: 30 mg/ml Taz2, 25 mM MES pH 6.3, 100 mM NaCl, 6% glycerol, 10% TCEP. Precipitating solution: 3.2 M AMS in MES buffer pH 6.0, 10 % ethylene glycol. Both solutions mixed 1:1 and kept under oil, Microbatch, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.2827 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2008 / Details: mirrors
RadiationMonochromator: Si 111 double, sagitally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 11355 / Num. obs: 11355 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 19.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1108 / Rsym value: 0.647 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-3000phasing
REFMAC5.4.0077refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→28.35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.234 / SU ML: 0.131 / TLS residual ADP flag: UNVERIFIED / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23639 543 4.8 %RANDOM
Rwork0.20646 ---
obs0.20802 10795 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.012 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 23 31 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021886
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9741185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.322.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.715179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.91511
X-RAY DIFFRACTIONr_chiral_restr0.1560.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021640
X-RAY DIFFRACTIONr_mcbond_it2.8653545
X-RAY DIFFRACTIONr_mcangle_it55873
X-RAY DIFFRACTIONr_scbond_it7.66341
X-RAY DIFFRACTIONr_scangle_it11.28312
LS refinement shellResolution: 2.5→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 49 -
Rwork0.274 758 -
obs--100 %
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)
17.3661-0.9209-0.11524.07520.2684.87780.18910.29260.6769-0.267-0.19140.0392-0.274-0.02890.00230.20520.05990.08690.2678-0.02740.183323.042895.801494.1824
29.6097-3.88330.94635.6596-0.98633.1227-0.04130.2006-0.6671-0.1332-0.03120.43770.4403-0.1180.07250.29120.03420.04130.3193-0.07220.024730.030380.702389.1321
34.8304-1.6471-2.68122.9428-0.57586.4708-0.1454-0.30680.51030.420.28250.15230.16370.4475-0.13710.27050.08580.04410.3039-0.0930.078130.258988.6236100.7494
45.19131.97825.75090.89391.75749.28310.25820.1701-0.1008-0.0191-0.1433-0.2083-0.03440.1988-0.11490.33760.0650.03650.2738-0.09070.061444.557783.2487115.6569
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1730 - 1747
2X-RAY DIFFRACTION2A1759 - 1770
3X-RAY DIFFRACTION3A1781 - 1794
4X-RAY DIFFRACTION4A1804 - 1833

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