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- PDB-5lpm: Crystal structure of the bromodomain of human Ep300 bound to the ... -

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Entry
Database: PDB / ID: 5lpm
TitleCrystal structure of the bromodomain of human Ep300 bound to the inhibitor XDM3d
ComponentsHistone acetyltransferase p300
KeywordsTRANSCRIPTION / bromodomain / protein-inhibitor complex / epigenetics
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
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-like / Histone Acetyltransferase; Chain A / 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
Chem-71Y / ACETATE ION / Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsHuegle, M. / Wohlwend, D. / Gerhardt, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWO2012/1-1 Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles.
Authors: Hugle, M. / Lucas, X. / Ostrovskyi, D. / Regenass, P. / Gerhardt, S. / Einsle, O. / Hau, M. / Jung, M. / Breit, B. / Gunther, S. / Wohlwend, D.
History
DepositionAug 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)29,3309
Polymers27,6542
Non-polymers1,6777
Water5,981332
1
A: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6955
Polymers13,8271
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6364
Polymers13,8271
Non-polymers8093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.861, 81.087, 44.779
Angle α, β, γ (deg.)90.000, 110.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13826.797 Da / Num. of mol.: 2 / Fragment: bromodomain, UNP residues 1048-1161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300, P300 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09472, histone acetyltransferase
#2: Chemical
ChemComp-71Y / ~{N}-[(1~{S},2~{S})-7-chloranyl-2-oxidanyl-1,2,3,4-tetrahydronaphthalen-1-yl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole -2-carboxamide / I-p300


Mass: 374.861 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23ClN2O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.33 Å3/Da / Density % sol: 47.14 % / Mosaicity: 0.14 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5 / Details: NaCl, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2016
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.37→41.922 Å / Num. obs: 52009 / % possible obs: 97.3 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.37-1.393.70.7320.672179.6
7.49-41.924.30.0270.996194.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å41.92 Å
Translation1.5 Å41.92 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.17data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo-p300

Resolution: 1.5→41.922 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.1871 1978 4.96 %
Rwork0.1579 --
obs0.1593 39914 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.91 Å2 / Biso mean: 25.782 Å2 / Biso min: 12.25 Å2
Refinement stepCycle: final / Resolution: 1.5→41.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 257 333 2535
Biso mean--28.1 34.76 -
Num. residues----232
Refinement TLS params.Method: refined / Origin x: 34.6733 Å / Origin y: 21.4205 Å / Origin z: 8.1528 Å
111213212223313233
T0.1586 Å2-0.0079 Å20.0354 Å2-0.1484 Å2-0.0007 Å2--0.1339 Å2
L1.1666 °2-0.3704 °20.6404 °2-0.4627 °2-0.2591 °2--1.1677 °2
S-0.0019 Å °-0.0204 Å °-0.0647 Å °-0.0548 Å °0.0528 Å °0.0114 Å °0.0209 Å °-0.0525 Å °-0.0542 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1046 - 1161
2X-RAY DIFFRACTION1allB1046 - 1161
3X-RAY DIFFRACTION1allC4 - 8
4X-RAY DIFFRACTION1allD1 - 3
5X-RAY DIFFRACTION1allW1 - 332

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