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- PDB-5fe9: Crystal structure of human PCAF bromodomain in complex with compo... -

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Basic information

Entry
Database: PDB / ID: 5fe9
TitleCrystal structure of human PCAF bromodomain in complex with compound SL1122 (compound 13)
ComponentsHistone acetyltransferase KAT2B
KeywordsSIGNALING 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 / 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 / peptidyl-lysine acetylation / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor ...regulation of protein ADP-ribosylation / negative regulation of rRNA processing / 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 / peptidyl-lysine acetylation / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / positive regulation of fatty acid biosynthetic process / actomyosin / 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 / A band / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / limb development / SAGA complex / NOTCH4 Intracellular Domain Regulates Transcription / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / regulation of tubulin deacetylation / protein-lysine-acetyltransferase activity / histone acetyltransferase binding / protein acetylation / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / histone acetyltransferase activity / Formation of paraxial mesoderm / acetyltransferase activity / regulation of RNA splicing / regulation of cell division / regulation of embryonic development / RNA Polymerase I Transcription Initiation / regulation of DNA repair / 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 / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / 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 / kinetochore / positive regulation of neuron projection development / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / memory / mitotic spindle / Metalloprotease DUBs / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to insulin stimulus / vasodilation / rhythmic process / HATs acetylate histones / heart development / 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
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-5WS / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2016
Title: Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain.
Authors: Chaikuad, A. / Lang, S. / Brennan, P.E. / Temperini, C. / Fedorov, O. / Hollander, J. / Nachane, R. / Abell, C. / Muller, S. / Siegal, G. / Knapp, S.
History
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jul 21, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Jan 10, 2024Group: 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 / 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)28,9395
Polymers28,3452
Non-polymers5953
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint0 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.076, 100.076, 99.821
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: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 723 - 831 / Label seq-ID: 11 - 119

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 / Fragment: UNP residues 715-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT2B, PCAF / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: Q92831, histone acetyltransferase
#2: Chemical ChemComp-5WS / ~{N}-(1,4-dimethyl-2-oxidanylidene-quinolin-7-yl)methanesulfonamide


Mass: 266.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.76 %
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54167 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54167 Å / Relative weight: 1
ReflectionResolution: 2.35→32.72 Å / Num. obs: 15504 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 47.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.4
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
PROTEUM PLUSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GG3

3gg3


Resolution: 2.35→32.72 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.691 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25828 776 5 %RANDOM
Rwork0.20094 ---
obs0.20365 14724 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.349 Å
Refinement stepCycle: 1 / Resolution: 2.35→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 40 116 1961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021903
X-RAY DIFFRACTIONr_bond_other_d0.0060.021798
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9982570
X-RAY DIFFRACTIONr_angle_other_deg1.1833.0044151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7045218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88223.79387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23915345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7641510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212083
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02443
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_it1.2863.045872
X-RAY DIFFRACTIONr_mcbond_other1.2853.042871
X-RAY DIFFRACTIONr_mcangle_it2.1794.5531087
X-RAY DIFFRACTIONr_mcangle_other2.1784.5581088
X-RAY DIFFRACTIONr_scbond_it1.7223.3271031
X-RAY DIFFRACTIONr_scbond_other1.7213.3271031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8774.9391483
X-RAY DIFFRACTIONr_long_range_B_refined6.25826.8452327
X-RAY DIFFRACTIONr_long_range_B_other6.25626.8692328
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12186 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 58 -
Rwork0.261 1051 -
obs--98.32 %
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)
111.864914.1167-0.014318.937-6.710821.1723-1.15720.4973-0.1829-0.8045-0.338-0.7621-1.4483.1761.49520.79140.1-0.15630.76230.02250.789118.560230.885989.431
24.6331-1.35660.93473.152-0.66363.1788-0.594-0.2262-0.2653-0.03460.55140.16880.06040.01780.04250.22710.06010.09980.19020.12650.1197-0.491225.462580.6007
318.15-4.01832.98556.25624.92266.30050.73861.504-1.98630.0009-0.20710.23270.28720.3703-0.53150.6806-0.3691-0.07780.4558-0.25210.3823-4.37825.233449.2955
44.41160.77010.08293.99310.61463.307-0.4290.0213-0.24790.01630.4263-0.0192-0.03330.16430.00270.1266-0.0568-0.06130.09860.06780.1037-1.21637.516763.3775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A723 - 728
2X-RAY DIFFRACTION2A729 - 831
3X-RAY DIFFRACTION3B723 - 734
4X-RAY DIFFRACTION4B735 - 831

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