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- PDB-9it5: p300 KAT domain in complex with KB528 -

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Basic information

Entry
Database: PDB / ID: 9it5
Titlep300 KAT domain in complex with KB528
ComponentsHistone acetyltransferase p300
KeywordsTRANSFERASE / KB528 / EP300 / P300 / HISTONE ACETYLTRANSFERASE
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 / Formation of paraxial mesoderm / histone H3K122 acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / acetyltransferase activity / FOXO-mediated transcription of cell death genes / PI5P Regulates TP53 Acetylation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / stimulatory C-type lectin receptor signaling pathway / fat cell differentiation / Zygotic genome activation (ZGA) / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone acetyltransferase activity / RUNX3 regulates p14-ARF / histone acetyltransferase complex / 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 / negative regulation of protein-containing complex assembly / pre-mRNA intronic binding / Attenuation phase / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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
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 ...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 / bromo domain / Bromodomain (BrD) profile. / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRahl, P. / Gao, H. / Calderon, Y. / Wang, Z.-F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma
Authors: Lenoir, F. / McKeown, M. / Giorgetti, G. / Kobylarz, M. / Hopkins, T. / Glore, W. / Shum, M. / Calderon, Y. / Carvajal, L. / Mori, K. / Gao, H. / Zhou, M. / Trotter, B. / Dinsmore, C. / ...Authors: Lenoir, F. / McKeown, M. / Giorgetti, G. / Kobylarz, M. / Hopkins, T. / Glore, W. / Shum, M. / Calderon, Y. / Carvajal, L. / Mori, K. / Gao, H. / Zhou, M. / Trotter, B. / Dinsmore, C. / Munshi, N. / Lin, C. / Fulciniti, M. / Mariateresa, F. / Rahl, P.
History
DepositionJul 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,09310
Polymers80,7842
Non-polymers1,3088
Water8,611478
1
A: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0465
Polymers40,3921
Non-polymers6544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area16520 Å2
MethodPISA
2
B: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0465
Polymers40,3921
Non-polymers6544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 164.933, 56.588
Angle α, β, γ (deg.)90.000, 111.845, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone acetyltransferase p300 / p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone ...p300 HAT / E1A-associated protein p300 / Histone butyryltransferase p300 / Histone crotonyltransferase p300 / Protein 2-hydroxyisobutyryltransferase p300 / Protein lactyltransferas p300 / Protein propionyltransferase p300


Mass: 40392.195 Da / Num. of mol.: 2 / Fragment: KAT domain / Mutation: K1637R/M1652G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Production host: Escherichia coli (E. coli)
References: UniProt: Q09472, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 5 types, 486 molecules

#2: Chemical ChemComp-A1L3B / 4-[(2~{S})-1-[[(~{R})-[(3~{S})-7-(1-methylpyrazol-4-yl)-2,3-dihydro-1~{H}-pyrido[2,3-b][1,4]oxazin-3-yl]-phenyl-methyl]amino]propan-2-yl]benzenecarbonitrile


Mass: 464.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H28N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: HM(PEGs-E9)-D6 (0.18M NH4Cl, 24% PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2→44.302 Å / Num. obs: 50921 / % possible obs: 98 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 10
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 1.085 / Num. unique obs: 3701

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.302 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.845 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2378 2644 5.198 %
Rwork0.1878 48226 -
all0.19 --
obs-50870 97.906 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.942 Å2
Baniso -1Baniso -2Baniso -3
1--1.279 Å20 Å20.951 Å2
2--0.293 Å2-0 Å2
3---0.169 Å2
Refinement stepCycle: LAST / Resolution: 2→44.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 92 478 5950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125686
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165328
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.8617695
X-RAY DIFFRACTIONr_angle_other_deg0.4641.78212331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.1665.57752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92210990
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.37210273
X-RAY DIFFRACTIONr_chiral_restr0.0650.2809
X-RAY DIFFRACTIONr_chiral_restr_other0.0410.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
X-RAY DIFFRACTIONr_nbd_refined0.2020.21074
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.24615
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22712
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2358
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0180.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.221
X-RAY DIFFRACTIONr_nbd_other0.1980.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.217
X-RAY DIFFRACTIONr_mcbond_it2.5063.672656
X-RAY DIFFRACTIONr_mcbond_other2.5053.672656
X-RAY DIFFRACTIONr_mcangle_it3.7726.583318
X-RAY DIFFRACTIONr_mcangle_other3.7726.583319
X-RAY DIFFRACTIONr_scbond_it3.034.0063030
X-RAY DIFFRACTIONr_scbond_other3.0294.0063031
X-RAY DIFFRACTIONr_scangle_it4.8677.1894367
X-RAY DIFFRACTIONr_scangle_other4.8667.1894368
X-RAY DIFFRACTIONr_lrange_it6.6139.3616430
X-RAY DIFFRACTIONr_lrange_other6.5538.3456347
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3311980.27834920.28138140.9320.95696.74880.278
2.052-2.1080.3131890.2734530.27237410.9370.95797.35370.27
2.108-2.1690.31960.2433710.24336830.9370.96496.85040.24
2.169-2.2360.2881790.22132170.22534780.9470.96797.64230.221
2.236-2.3090.2971750.21931410.22334020.9410.96997.47210.219
2.309-2.3890.2491660.20531000.20833430.9620.97397.69670.205
2.389-2.4790.2731770.22229180.22531610.9470.96897.91210.222
2.479-2.580.2661500.19928580.20330720.9560.97397.91670.199
2.58-2.6950.271270.18827780.19229630.9580.97798.04250.188
2.695-2.8260.2191380.18626400.18828270.9680.97898.26670.186
2.826-2.9780.2341510.20224630.20426520.960.97498.56710.202
2.978-3.1570.2331330.18223760.18525490.9670.98198.43080.182
3.157-3.3740.2391080.19622450.19923900.9680.97798.45190.196
3.374-3.6430.241160.18520790.18822210.9630.9898.82940.185
3.643-3.9880.2441100.16319020.16820400.9620.98498.62740.163
3.988-4.4540.182720.13817720.1418800.9820.98798.08510.138
4.454-5.1340.144810.14115410.14116390.9890.98998.96280.141
5.134-6.2670.212740.17712970.17913870.9830.98798.84640.177
6.267-8.7760.196600.17410060.17510850.9820.98498.24880.174
8.776-44.3020.263440.1975770.2016280.9710.98198.88540.197

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