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- PDB-4bhw: Structural basis for autoinhibition of the acetyltransferase acti... -

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Basic information

Entry
Database: PDB / ID: 4bhw
TitleStructural basis for autoinhibition of the acetyltransferase activity of p300
ComponentsHISTONE ACETYLTRANSFERASE P300
KeywordsTRANSFERASE / BROMODOMAIN / PHD DOMAIN / RING DOMAIN / HAT DOMAIN / ENHANCEOSOME
Function / homologyBromodomain / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Creb binding / Bromodomain signature. / Zinc finger ZZ-type signature. / Bromodomain profile. / Zinc finger TAZ-type profile. / Zinc finger ZZ-type profile. / KIX domain profile. / Regulation of gene expression by Hypoxia-inducible Factor ...Bromodomain / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Creb binding / Bromodomain signature. / Zinc finger ZZ-type signature. / Bromodomain profile. / Zinc finger TAZ-type profile. / Zinc finger ZZ-type profile. / KIX domain profile. / Regulation of gene expression by Hypoxia-inducible Factor / Domain of Unknown Function (DUF902) / RORA activates gene expression / Polo-like kinase mediated events / Pre-NOTCH Transcription and Translation / PPARA activates gene expression / Zinc finger, ZZ-type / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / NOTCH1 Intracellular Domain Regulates Transcription / Histone acetylation protein / KIX domain / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Zinc finger, TAZ-type / Coactivator CBP, KIX domain / Nuclear receptor coactivator, interlocking / CREB-binding protein/p300, atypical RING domain / Zinc finger, RING/FYVE/PHD-type / Histone acetyltransferase Rtt109/CBP / Nuclear receptor coactivator, CREB-bp-like, interlocking / Bromodomain, conserved site / CBP/p300-type histone acetyltransferase domain / TAZ zinc finger / TAZ domain superfamily / Bromodomain-like superfamily / Coactivator CBP, KIX domain superfamily / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / CBP/p300, atypical RING domain superfamily / Bromodomain / Zinc finger, ZZ type / NOTCH2 intracellular domain regulates transcription / Formation of the beta-catenin:TCF transactivating complex / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of RUNX3 expression and activity / Regulation of TP53 Activity through Acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / PI5P Regulates TP53 Acetylation / Activation of the TFAP2 (AP-2) family of transcription factors / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX3 regulates NOTCH signaling / RUNX3 regulates p14-ARF / Gap-filling DNA repair synthesis and ligation in TC-NER / NOTCH3 Intracellular Domain Regulates Transcription / NOTCH4 Intracellular Domain Regulates Transcription / Estrogen-dependent gene expression / TRAF3-dependent IRF activation pathway / TRAF6 mediated IRF7 activation / FOXO-mediated transcription of cell death genes / Regulation of FOXO transcriptional activity by acetylation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Regulation of TP53 Activity through Methylation / Dual incision in TC-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Metalloprotease DUBs / HATs acetylate histones / CD209 (DC-SIGN) signaling / Attenuation phase / Transcriptional regulation of white adipocyte differentiation / SUMOylation of transcription cofactors / Circadian Clock / Activation of anterior HOX genes in hindbrain development during early embryogenesis / B-WICH complex positively regulates rRNA expression / peptide butyryltransferase activity / peptidyl-lysine crotonylation / histone crotonyltransferase activity / behavioral defense response / histone H2B acetylation / protein propionyltransferase activity / peptidyl-lysine propionylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response / swimming / regulation of tubulin deacetylation / thigmotaxis / peptide-lysine-N-acetyltransferase activity / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / STAT family protein binding / regulation of androgen receptor signaling pathway / peptide N-acetyltransferase activity / positive regulation by host of viral transcription / positive regulation of gene expression, epigenetic / somitogenesis / internal peptidyl-lysine acetylation / internal protein amino acid acetylation / N-terminal peptidyl-lysine acetylation / megakaryocyte development / pre-mRNA intronic binding
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.799 Å resolution
AuthorsDelvecchio, M. / Gaucher, J. / Aguilar-Gurrieri, C. / Ortega, E. / Panne, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of the P300 Catalytic Core and Implications for Chromatin Targeting and Hat Regulation
Authors: Delvecchio, M. / Gaucher, J. / Aguilar-Gurrieri, C. / Ortega, E. / Panne, D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 8, 2013 / Release: Aug 14, 2013
RevisionDateData content typeGroupProviderType
1.0Aug 14, 2013Structure modelrepositoryInitial release
1.1Aug 21, 2013Structure modelDatabase references
1.2Sep 18, 2013Structure modelDatabase references

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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)136,65311
Polyers134,2052
Non-polymers2,4479
Water1,47782
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)1410
ΔGint (kcal/M)-116.4
Surface area (Å2)57350
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)153.051, 92.894, 123.309
Angle α, β, γ (deg.)90.00, 98.43, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide HISTONE ACETYLTRANSFERASE P300 / P300 HAT / E1A-ASSOCIATED PROTEIN P300


Mass: 67102.695 Da / Num. of mol.: 2 / Fragment: P300 CORE, RESIDUES 1043-1519,1581-1666 / Mutation: YES / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HIGH FIVE CELLS / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q09472, histone acetyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc
#3: Chemical ChemComp-01K / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (3R,20R)-20-carbamoyl-3-hydroxy-2,2-dimethyl-4,8,14,22-tetraoxo-12-thia-5,9,15,21-tetraazatricos-1-yl dihydrogen diphosphate / Lysine-COENZYME A derivative


Mass: 994.794 Da / Num. of mol.: 2 / Formula: C31H53N10O19P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Formula: H2O / Water

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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: 3 / Density percent sol: 62 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES, PH 7.5, 20% PEG3350, 0.2M NACL

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.282
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Sep 9, 2011
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionD resolution high: 2.8 Å / D resolution low: 5 Å / Number obs: 80344 / Observed criterion sigma I: 2 / Rmerge I obs: 0.07 / NetI over sigmaI: 9.4 / Redundancy: 3.4 % / Percent possible obs: 97.4
Reflection shellRmerge I obs: 0.59 / Highest resolution: 2.8 Å / Lowest resolution: 2.85 Å / MeanI over sigI obs: 1.5 / Redundancy: 3.3 % / Percent possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefineMethod to determine structure: SAD
Starting model: PDB ENTRY 3BIY
Overall SU ML: 0.37 / Sigma F: 1.2 / Overall phase error: 25.28 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.98 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 27.313 / Solvent model param ksol: 0.274
Displacement parametersAniso B11: -2.097 Å2 / Aniso B12: 0 Å2 / Aniso B13: 1.3803 Å2 / Aniso B22: 8.8622 Å2 / Aniso B23: - Å2 / Aniso B33: -6.7652 Å2
Least-squares processR factor R free: 0.2441 / R factor R work: 0.2077 / R factor obs: 0.2096 / Highest resolution: 2.799 Å / Lowest resolution: 46.62 Å / Number reflection R free: 4056 / Number reflection obs: 80344 / Percent reflection R free: 5.1 / Percent reflection obs: 97.05
Refine hist #LASTHighest resolution: 2.799 Å / Lowest resolution: 46.62 Å
Number of atoms included #LASTProtein: 9177 / Nucleic acid: 0 / Ligand: 135 / Solvent: 82 / Total: 9394
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069595
X-RAY DIFFRACTIONf_angle_d1.10213011
X-RAY DIFFRACTIONf_dihedral_angle_d14.5473626
X-RAY DIFFRACTIONf_chiral_restr0.2331349
X-RAY DIFFRACTIONf_plane_restr0.0031678
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.79890.34220.34182.831898206377.00
2.83180.37340.34512.8663138263597.00
2.86630.37130.29482.9026138257094.00
2.90260.26400.29592.9408117259898.00
2.94080.37200.28752.9810144267795.00
2.98100.32510.28503.0236156253596.00
3.02360.35800.28163.0688132258296.00
3.06880.29430.26823.1167118260395.00
3.11670.31730.26833.1678163261297.00
3.16780.26650.25593.2224134258995.00
3.22240.26740.26503.2810136259997.00
3.28100.31530.26623.3441147260296.00
3.34410.30980.24243.4123161261598.00
3.41230.32140.25843.4865132258896.00
3.48650.25990.23273.5675157265697.00
3.56750.27120.22583.6567128267698.00
3.65670.24880.21613.7556130267597.00
3.75560.21740.19793.8660132272599.00
3.86600.21290.19553.9907150260799.00
3.99070.24250.17774.13331692696100.00
4.13330.18490.16994.29871442709100.00
4.29870.23050.14884.49421422726100.00
4.49420.17310.16054.73091282711100.00
4.73090.19060.17475.02701372684100.00
5.02700.25290.20205.41461332708100.00
5.41460.23690.20435.95851412780100.00
5.95850.27120.20956.81841752651100.00
6.81840.18680.16508.58171322707100.00
8.58170.18310.164346.6262144270999.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.5198-0.31990.08650.1570-0.02800.4836-0.05300.11130.1460-0.3445-0.19290.0241-0.2472-0.6902-0.32320.83460.4330-0.07150.98010.09240.5263-48.43615.903025.5646
20.38290.05900.0107-0.0450-0.16950.2091-0.07410.42100.04200.0001-0.33010.48950.5507-0.2928-0.06590.8275-0.03490.20010.4230-0.02460.6089-59.2603-11.664554.3268
30.28270.3559-0.36691.4117-0.66231.19070.08280.00490.0416-0.0534-0.11610.01420.0784-0.0828-0.06760.0838-0.0005-0.03510.21850.00840.2830-27.9293-19.640856.9861
40.30930.11740.43800.37570.21230.85890.2988-0.06840.24340.0422-0.36420.02840.0273-0.83770.03160.13370.16630.04100.36700.05620.5324-34.5730-3.638354.6135
50.26890.1296-0.09930.1263-0.21180.2524-0.05820.1854-0.11960.0096-0.11920.13270.5050-0.6760-0.00021.0021-0.31970.08650.9396-0.01200.5819-50.7295-40.745133.3945
60.0865-0.05780.0876-0.1115-0.0801-0.01240.0811-0.07330.1621-0.1325-0.37790.4224-0.2653-0.1807-0.00011.17870.1276-0.15430.7152-0.06680.7200-53.6166-23.86942.6811
7-0.0900-0.0034-0.10611.2243-0.22741.33910.00890.0110-0.0214-0.1921-0.1387-0.15250.13630.1011-0.00160.44010.10370.06670.34720.05910.3209-20.9561-17.977910.6488
80.24620.10400.09000.5034-0.31520.33690.12670.11240.0203-0.2481-0.1631-0.05940.1301-0.11120.00000.70650.06740.07980.4587-0.01240.4052-23.5110-17.82015.8442
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1046:1179)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 1180:1243)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 1244:1621)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 1622:1664)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 1046:1179)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 1180:1243)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 1244:1520)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 1521:1664)

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