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- PDB-5lvq: Crystal structure of human PCAF bromodomain in complex with compo... -

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Basic information

Entry
Database: PDB / ID: 5lvq
TitleCrystal structure of human PCAF bromodomain in complex with compound-D (CPD-D), N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide
ComponentsHistone acetyltransferase KAT2B
KeywordsTRANSFERASE / SIGNALING PROTEIN / BROMODOMAIN / HISTONE ACETYLTRANSFERASE KAT2B / HISTONE / ACETYLATION / ACETYLLYSINE / EPIGENETICS / STRUCTURAL GENOMICS CONSORTIUM (SGC)
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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / peptidyl-lysine acetylation ...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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / actomyosin / positive regulation of fatty acid biosynthetic process / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / I band / cellular response to parathyroid hormone stimulus / Regulation of FOXO transcriptional activity by acetylation / limb development / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / A band / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / histone acetyltransferase binding / protein acetylation / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / regulation of DNA repair / histone acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / positive regulation of glycolytic process / transcription initiation-coupled chromatin remodeling / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription coregulator activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / memory / kinetochore / Pre-NOTCH Transcription and Translation / histone deacetylase binding / positive regulation of neuron projection development / cellular response to insulin stimulus / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / vasodilation / rhythmic process / heart development / HATs acetylate histones / cellular response to oxidative stress / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / 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
N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsChaikuad, A. / Filippakopoulos, P. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Hopkins, A.L. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: ACS Med Chem Lett / Year: 2016
Title: Discovery of New Bromodomain Scaffolds by Biosensor Fragment Screening.
Authors: Navratilova, I. / Aristotelous, T. / Picaud, S. / Chaikuad, A. / Knapp, S. / Filappakopoulos, P. / Hopkins, A.L.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9689
Polymers28,3452
Non-polymers6247
Water2,288127
1
A: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5945
Polymers14,1721
Non-polymers4214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3754
Polymers14,1721
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.859, 99.859, 100.762
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 724 - 829 / Label seq-ID: 12 - 117

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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


Mass: 14172.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2B, PCAF / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-pRARE2 / References: UniProt: Q92831, histone acetyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-2LX / N-methyl-2-(tetrahydro-2H-pyran-4-yloxy)benzamide


Mass: 235.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.41 Å3/Da / Density % sol: 63.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91997 Å / Relative weight: 1
ReflectionResolution: 2.05→65.62 Å / Num. obs: 23526 / % possible obs: 100 % / Redundancy: 4.8 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.9
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.05→43.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.543 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21795 1212 5.2 %RANDOM
Rwork0.18045 ---
obs0.18235 22306 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.896 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.05→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 41 127 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191903
X-RAY DIFFRACTIONr_bond_other_d0.0060.021808
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9772556
X-RAY DIFFRACTIONr_angle_other_deg1.20234184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9323.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1771511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212124
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02447
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_it3.7784.21871
X-RAY DIFFRACTIONr_mcbond_other3.7764.212872
X-RAY DIFFRACTIONr_mcangle_it5.3166.2731087
X-RAY DIFFRACTIONr_mcangle_other5.3156.2761088
X-RAY DIFFRACTIONr_scbond_it4.8664.7461032
X-RAY DIFFRACTIONr_scbond_other4.8644.7471033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1556.8941466
X-RAY DIFFRACTIONr_long_range_B_refined9.81534.9732345
X-RAY DIFFRACTIONr_long_range_B_other9.81434.9862346
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5972 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 86 -
Rwork0.294 1652 -
obs--99.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1546-0.15971.68993.65440.71661.37020.36940.09670.12430.2705-0.51270.04120.1513-0.10360.14330.1211-0.0479-0.00210.1893-0.0430.041821.731912.829953.5073
22.89940.1043-0.52083.55230.89412.96680.06960.3222-0.07220.2539-0.03480.4934-0.06910.0525-0.03480.0802-0.0258-0.01440.05320.00260.139132.59817.24672.2592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A724 - 831
2X-RAY DIFFRACTION2B723 - 830

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