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- PDB-4nsq: Crystal structure of PCAF -

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Basic information

Entry
Database: PDB / ID: 4nsq
TitleCrystal structure of PCAF
ComponentsHistone acetyltransferase KAT2B
KeywordsTRANSFERASE / acetyltransferase / COA Binding
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 / 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 / Physiological factors / positive regulation of attachment of mitotic spindle microtubules to kinetochore / peptidyl-lysine acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / 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 / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / SAGA complex / RUNX3 regulates NOTCH signaling / limb development / A band / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of FOXO transcriptional activity by acetylation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of tubulin deacetylation / peptide-lysine-N-acetyltransferase activity / histone acetyltransferase binding / protein acetylation / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / Formation of paraxial mesoderm / regulation of RNA splicing / 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 / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / kinetochore / mitotic spindle / memory / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of neuron projection development / cellular response to insulin stimulus / vasodilation / histone deacetylase binding / 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) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...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) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3108 Å
AuthorsLin, J.Y. / Cai, Y.F.
CitationJournal: Bmc Struct.Biol. / Year: 2014
Title: Dimeric structure of p300/CBP associated factor.
Authors: Shi, S. / Lin, J. / Cai, Y. / Yu, J. / Hong, H. / Ji, K. / Downey, J.S. / Lu, X. / Chen, R. / Han, J. / Han, A.
History
DepositionNov 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
C: Histone acetyltransferase KAT2B
D: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4248
Polymers87,3544
Non-polymers3,0704
Water0
1
A: Histone acetyltransferase KAT2B
D: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2124
Polymers43,6772
Non-polymers1,5352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-10 kcal/mol
Surface area16140 Å2
MethodPISA
2
B: Histone acetyltransferase KAT2B
C: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2124
Polymers43,6772
Non-polymers1,5352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-10 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.570, 65.570, 187.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 21838.416 Da / Num. of mol.: 4 / Fragment: UNP Residues 493-658
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
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 0.2M Lithium Sulfate, 0.1M HEPES pH7.4, 1.2M Ammonium Sulfate and 10mM Trimethylamine HCl, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 30459 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.31-2.35157.8
2.35-2.39166.3
2.39-2.44175.3
2.44-2.49196.4
2.49-2.54197.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3108→45.256 Å / SU ML: 0.73 / σ(F): 2 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 1854 6.09 %RANDOM
Rwork0.2288 ---
all0.2317 32806 --
obs0.2288 30459 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.081 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.5839 Å20 Å2-0 Å2
2--11.5839 Å20 Å2
3----23.1677 Å2
Refinement stepCycle: LAST / Resolution: 2.3108→45.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5104 0 192 0 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145436
X-RAY DIFFRACTIONf_angle_d1.1057340
X-RAY DIFFRACTIONf_dihedral_angle_d27.2383428
X-RAY DIFFRACTIONf_chiral_restr0.077776
X-RAY DIFFRACTIONf_plane_restr0.007884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3108-2.37330.353960.32431349X-RAY DIFFRACTION55
2.3733-2.44310.36091170.30421732X-RAY DIFFRACTION69
2.4431-2.5220.38121320.31042012X-RAY DIFFRACTION81
2.522-2.61210.38291370.31642073X-RAY DIFFRACTION84
2.6121-2.71670.38911380.34011961X-RAY DIFFRACTION79
2.7167-2.84030.38761400.30192307X-RAY DIFFRACTION92
2.8403-2.990.32451530.28252403X-RAY DIFFRACTION96
2.99-3.17730.33511530.2772420X-RAY DIFFRACTION98
3.1773-3.42260.28811610.25172451X-RAY DIFFRACTION98
3.4226-3.76680.27711600.22182458X-RAY DIFFRACTION99
3.7668-4.31160.26091570.19442494X-RAY DIFFRACTION99
4.3116-5.43070.22451630.18632500X-RAY DIFFRACTION100
5.4307-45.26460.2361470.21412445X-RAY DIFFRACTION97

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