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- PDB-5lkz: Crystal structure of the p300 acetyltransferase catalytic core wi... -

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Basic information

Entry
Database: PDB / ID: 5lkz
TitleCrystal structure of the p300 acetyltransferase catalytic core with crotonyl-coenzyme A.
ComponentsHistone acetyltransferase p300,Histone acetyltransferase p300
KeywordsTRANSFERASE / p300 acetyltransferase / crotonyl-CoA / chromatin modification / acylation
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 / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / thigmotaxis / 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 / 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 / host-mediated activation of viral transcription / TGFBR3 expression / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / face morphogenesis / 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 / nuclear androgen receptor binding / acyltransferase activity / STAT family protein binding / protein acetylation / histone H3K122 acetyltransferase activity / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / FOXO-mediated transcription of cell death genes / histone H3K18 acetyltransferase activity / PI5P Regulates TP53 Acetylation / histone H3K27 acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / fat cell differentiation / Zygotic genome activation (ZGA) / histone acetyltransferase activity / histone acetyltransferase complex / RUNX3 regulates p14-ARF / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / NF-kappaB binding / negative regulation of gluconeogenesis / pre-mRNA intronic binding / Attenuation phase / negative regulation of protein-containing complex assembly / somitogenesis / positive regulation of T-helper 17 cell lineage commitment / cellular response to nutrient levels / skeletal muscle tissue development / histone acetyltransferase / regulation of cellular response to heat / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of DNA-binding transcription factor activity / Regulation of TP53 Activity through Acetylation / : / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / negative regulation of autophagy / B cell differentiation / transcription initiation-coupled chromatin remodeling / SUMOylation of transcription cofactors / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest
Similarity search - Function
CREB-binding protein/p300 RING domain / Cysteine Rich Protein / 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/p300 RING domain / Cysteine Rich Protein / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Nuclear receptor coactivator, interlocking / Bromodomain-like / Histone Acetyltransferase; Chain A / Ribbon / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CROTONYL COENZYME A / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKaczmarska, Z. / Ortega, E. / Marquez, J.A. / Panne, D.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structure of p300 in complex with acyl-CoA variants.
Authors: Kaczmarska, Z. / Ortega, E. / Goudarzi, A. / Huang, H. / Kim, S. / Marquez, J.A. / Zhao, Y. / Khochbin, S. / Panne, D.
History
DepositionJul 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 28, 2016Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase p300,Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4769
Polymers67,1031
Non-polymers1,3748
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-22 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.600, 155.910, 110.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1953-

HOH

21A-1958-

HOH

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Components

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


Mass: 67102.695 Da / Num. of mol.: 1
Fragment: UNP residues 1043-1519,UNP residues 1581-1666,UNP residues 1043-1519,UNP residues 1581-1666
Mutation: Y1467F,Y1467F,Y1467F,Y1467F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09472, histone acetyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O17P3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Tris, PEG MME 2000 / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 28182 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rrim(I) all: 0.165 / Net I/σ(I): 9.93
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.81 / Rrim(I) all: 1.047 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BHW

4bhw


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.905 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23386 1336 4.7 %RANDOM
Rwork0.19846 ---
obs0.20014 26845 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.694 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å2-0 Å2
2---0.76 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4474 0 75 158 4707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194683
X-RAY DIFFRACTIONr_bond_other_d0.0020.024346
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9676328
X-RAY DIFFRACTIONr_angle_other_deg0.9483.00310036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96123.514222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87115802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1931532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021083
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2184.8432198
X-RAY DIFFRACTIONr_mcbond_other2.2154.8412197
X-RAY DIFFRACTIONr_mcangle_it3.7997.2382741
X-RAY DIFFRACTIONr_mcangle_other3.7997.2412742
X-RAY DIFFRACTIONr_scbond_it2.2224.9742484
X-RAY DIFFRACTIONr_scbond_other2.2214.9742484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8137.3533585
X-RAY DIFFRACTIONr_long_range_B_refined6.640.1789668
X-RAY DIFFRACTIONr_long_range_B_other6.57540.1969632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 87 -
Rwork0.293 1952 -
obs--100 %

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