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- PDB-6j3o: Crystal structure of the human PCAF bromodomain in complex with c... -

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Basic information

Entry
Database: PDB / ID: 6j3o
TitleCrystal structure of the human PCAF bromodomain in complex with compound 12
ComponentsHistone acetyltransferase KAT2B
KeywordsTRANSFERASE / Crystal structure of the human PCAF bromodomain in complex with compound 12
Function / homology
Function and homology information


regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / peptidyl-lysine acetylation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / histone H3 acetyltransferase activity / positive regulation of fatty acid biosynthetic process / actomyosin / internal peptidyl-lysine acetylation / cyclin-dependent protein serine/threonine kinase inhibitor activity / ATAC complex / N-terminal peptidyl-lysine acetylation / I band / SAGA complex / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / limb development / RUNX3 regulates NOTCH signaling / A band / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / NOTCH3 Intracellular Domain Regulates Transcription / histone acetyltransferase binding / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / regulation of cell division / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / protein acetylation / regulation of RNA splicing / Formation of paraxial mesoderm / acetyltransferase activity / RNA Polymerase I Transcription Initiation / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / positive regulation of gluconeogenesis / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / positive regulation of neuron projection development / Metalloprotease DUBs / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / memory / kinetochore / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Pre-NOTCH Transcription and Translation / vasodilation / histone deacetylase binding / cellular response to insulin stimulus / rhythmic process / cellular response to oxidative stress / heart development / HATs acetylate histones / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-B4L / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsHuang, L.Y. / Li, H. / Li, L.L. / Niu, L. / Seupel, R. / Wu, C.Y. / Li, G.B. / Yu, Y.M. / Brennan, P.E. / Yang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81473140, 81573349, 81773633, and 21772130 China
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of Pyrrolo[3,2- d]pyrimidin-4-one Derivatives as a New Class of Potent and Cell-Active Inhibitors of P300/CBP-Associated Factor Bromodomain.
Authors: Huang, L. / Li, H. / Li, L. / Niu, L. / Seupel, R. / Wu, C. / Cheng, W. / Chen, C. / Ding, B. / Brennan, P.E. / Yang, S.
History
DepositionJan 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / citation_author / computing / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / refine / reflns / reflns_shell / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _computing.structure_refinement / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_Rpim_I_all / _software.version
Revision 2.1Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT2B
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8114
Polymers33,2882
Non-polymers5232
Water79344
1
A: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9052
Polymers16,6441
Non-polymers2611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9052
Polymers16,6441
Non-polymers2611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.520, 101.520, 99.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Histone acetyltransferase KAT2B / Histone acetyltransferase PCAF / Histone acetylase PCAF / Lysine acetyltransferase 2B / P300/CBP- ...Histone acetyltransferase PCAF / Histone acetylase PCAF / Lysine acetyltransferase 2B / P300/CBP-associated factor / P/CAF / Spermidine acetyltransferase KAT2B


Mass: 16644.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2B, PCAF / Production host: Escherichia coli (E. coli)
References: UniProt: Q92831, histone acetyltransferase, diamine N-acetyltransferase
#2: Chemical ChemComp-B4L / 3-methyl-2-[[(3~{R})-1-methylpiperidin-3-yl]amino]-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one


Mass: 261.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES pH 8.2, 26% PEG10000 (v/v), 4% glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978897 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978897 Å / Relative weight: 1
ReflectionResolution: 2.11→50.76 Å / Num. obs: 21934 / % possible obs: 99.6 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.5
Reflection shellResolution: 2.11→2.17 Å / Rmerge(I) obs: 1.553

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Processing

Software
NameVersionClassification
PHENIX(1.14RC3_3199: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MKX

5mkx


Resolution: 2.11→50.76 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.82
RfactorNum. reflection% reflection
Rfree0.257 1996 9.13 %
Rwork0.23 --
obs0.233 21873 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.11→50.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 38 44 1834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021851
X-RAY DIFFRACTIONf_angle_d0.5052501
X-RAY DIFFRACTIONf_dihedral_angle_d16.831119
X-RAY DIFFRACTIONf_chiral_restr0.035257
X-RAY DIFFRACTIONf_plane_restr0.003311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1104-2.16320.39831400.36171414X-RAY DIFFRACTION99
2.1632-2.22170.39251450.37861418X-RAY DIFFRACTION99
2.2217-2.2870.62881250.53931333X-RAY DIFFRACTION94
2.287-2.36090.3781410.3381436X-RAY DIFFRACTION100
2.3609-2.44520.36361460.28421436X-RAY DIFFRACTION100
2.4452-2.54310.32331470.28681449X-RAY DIFFRACTION100
2.5431-2.65890.36591390.28691398X-RAY DIFFRACTION100
2.6589-2.79910.33731500.28091450X-RAY DIFFRACTION100
2.7991-2.97440.32161420.25791413X-RAY DIFFRACTION100
2.9744-3.2040.27641450.24721432X-RAY DIFFRACTION100
3.204-3.52640.23761460.22361428X-RAY DIFFRACTION100
3.5264-4.03650.2141460.19361422X-RAY DIFFRACTION100
4.0365-5.08480.21291410.18381430X-RAY DIFFRACTION100
5.0848-50.77470.19251430.18861418X-RAY DIFFRACTION99

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