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- PDB-5fe4: Crystal structure of human PCAF bromodomain in complex with fragm... -

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Basic information

Entry
Database: PDB / ID: 5fe4
TitleCrystal structure of human PCAF bromodomain in complex with fragment MB364 (fragment 5)
ComponentsHistone acetyltransferase KAT2B
KeywordsSIGNALING PROTEIN / bromodomain / Histone acetyltransferase KAT2B / histone / acetylation / acetyllysine / epigenetics / structural genomics consortium (SGC)
Function / homology
Function and homology information


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 / A band / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor ...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 / A band / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / YAP1- and WWTR1 (TAZ)-stimulated gene expression / internal peptidyl-lysine acetylation / positive regulation of fatty acid biosynthetic process / histone H3 acetyltransferase activity / actomyosin / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / I band / limb development / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / protein-lysine-acetyltransferase activity / negative regulation of ferroptosis / protein acetylation / Notch-HLH transcription pathway / histone acetyltransferase binding / Formation of WDR5-containing histone-modifying complexes / Formation of paraxial mesoderm / acetyltransferase activity / regulation of RNA splicing / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / histone acetyltransferase activity / regulation of DNA repair / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / enzyme activator activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of neuron projection development / kinetochore / B-WICH complex positively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / vasodilation / Metalloprotease DUBs / memory / histone deacetylase binding / cellular response to insulin stimulus / mitotic spindle / 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 / nucleus / cytoplasm / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-dihydro-1,4-benzodioxine-5-carboxamide / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.2Jan 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)29,0139
Polymers28,3452
Non-polymers6697
Water3,855214
1
A: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4764
Polymers14,1721
Non-polymers3033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5385
Polymers14,1721
Non-polymers3654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.252, 99.252, 100.612
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: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 724 - 831 / Label seq-ID: 12 - 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: PCAF bromodomain, 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-5WY / 2,3-dihydro-1,4-benzodioxine-5-carboxamide


Mass: 179.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
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: 1.54197 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Sep 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54197 Å / Relative weight: 1
ReflectionResolution: 2.15→32.68 Å / Num. obs: 19803 / % possible obs: 98.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.2
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2 / % possible all: 95.5

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Processing

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

3gg3


Resolution: 2.15→28.65 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.32 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23175 1008 5.1 %RANDOM
Rwork0.18934 ---
obs0.1915 18793 98.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---1.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.336 Å
Refinement stepCycle: 1 / Resolution: 2.15→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 46 214 2060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021918
X-RAY DIFFRACTIONr_bond_other_d0.0070.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9942577
X-RAY DIFFRACTIONr_angle_other_deg1.3433.0064235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70123.93389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30615356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7291510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212092
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02446
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_it1.1252.227870
X-RAY DIFFRACTIONr_mcbond_other1.1212.224869
X-RAY DIFFRACTIONr_mcangle_it1.8643.3221086
X-RAY DIFFRACTIONr_mcangle_other1.8643.3261087
X-RAY DIFFRACTIONr_scbond_it1.4392.4431048
X-RAY DIFFRACTIONr_scbond_other1.4382.4461049
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2953.5731488
X-RAY DIFFRACTIONr_long_range_B_refined6.72419.4462426
X-RAY DIFFRACTIONr_long_range_B_other6.72319.4582427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11896 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 81 -
Rwork0.251 1355 -
obs--95.61 %
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)
141.8058-20.9141-0.376742.762523.0516.18490.3458-0.1321-1.0249-0.3995-0.11110.1662-0.1681-0.1155-0.23470.3411-0.0157-0.02940.30080.10180.272933.2553-16.921855.0257
215.0253-7.90286.28289.50984.22413.2169-0.19590.52130.31290.0533-0.0798-0.0734-0.19040.4690.27570.23820.0062-0.0670.26060.09440.283530.6729-13.653251.8443
37.59450.85952.05162.37650.06823.03830.345-0.7153-0.17850.091-0.16-0.115-0.0076-0.1912-0.1850.0226-0.0274-0.01550.0939-0.01780.077414.9132-5.595641.329
44.55860.8784-0.02154.2584-1.48295.18550.2385-0.1747-0.5518-0.1008-0.0816-0.39730.18480.2713-0.15690.0249-0.0073-0.00870.0357-0.02530.188320.4515-10.297837.6106
59.68170.99389.07790.15981.03358.71080.405-0.0238-0.1357-0.0037-0.1753-0.04870.3566-0.3365-0.22970.32950.04970.06380.54320.05710.305315.0343-28.834711.0928
62.39960.3166-0.78146.46141.12043.8090.0134-0.3695-0.0689-0.1435-0.0785-0.22570.06220.14740.06520.09110.05110.10050.1350.02230.161529.1554-15.654821.0483
75.4523-1.8848-2.76595.42890.19047.1806-0.1467-0.1709-0.2063-0.15990.1228-0.01060.2190.08120.0240.2025-0.0011-0.01350.2512-0.03540.205313.1218-14.962318.1482
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A724 - 726
2X-RAY DIFFRACTION2A727 - 729
3X-RAY DIFFRACTION3A730 - 761
4X-RAY DIFFRACTION4A762 - 831
5X-RAY DIFFRACTION5B724 - 729
6X-RAY DIFFRACTION6B730 - 822
7X-RAY DIFFRACTION7B823 - 831

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