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- PDB-1cm0: CRYSTAL STRUCTURE OF THE PCAF/COENZYME-A COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1cm0
TitleCRYSTAL STRUCTURE OF THE PCAF/COENZYME-A COMPLEX
ComponentsP300/CBP ASSOCIATING FACTOR
KeywordsSIGNALING PROTEIN / P300/CBP ASSOCIATED FACTOR / COENZYME A / ACETYLTRANSFERASE / COACTIVATOR
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) / 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: 2.3 Å
AuthorsClements, A. / Rojas, J.R. / Trievel, R.C. / Wang, L. / Berger, S.L. / Marmorstein, R.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of the histone acetyltransferase domain of the human PCAF transcriptional regulator bound to coenzyme A.
Authors: Clements, A. / Rojas, J.R. / Trievel, R.C. / Wang, L. / Berger, S.L. / Marmorstein, R.
History
DepositionMay 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: P300/CBP ASSOCIATING FACTOR
A: P300/CBP ASSOCIATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5534
Polymers39,0182
Non-polymers1,5352
Water1,964109
1
B: P300/CBP ASSOCIATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2762
Polymers19,5091
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: P300/CBP ASSOCIATING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2762
Polymers19,5091
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.000, 97.000, 77.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein P300/CBP ASSOCIATING FACTOR


Mass: 19508.889 Da / Num. of mol.: 2 / Fragment: HISTONE ACETYLTRANSFERASE DOMAIN
Source method: isolated from a genetically manipulated source
Details: COCRYSTALLIZED WITH COENZYME A / Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUSCell nucleus / Plasmid: PRSET A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92831
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.8 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5MG/ML OF P/CAF WITH 2 M EXCESS COFACTOR, 100MM TRIS, 1.5 M LITHIUM SULFATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
31.3-1.6 M1reservoirLiSO4
40.1 MTris-HCl1reservoir
2cofactor1drop2-fold molar excess

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.009
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 17943 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 41.6 Å2 / Rsym value: 4 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.7 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 4.8 / Rsym value: 15.5 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 94731 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.155

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APOTGCN5

Resolution: 2.3→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1761 10 %RANDOM
Rwork0.223 ---
obs-17925 96.5 %-
Solvent computationBsol: 39 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å2-7.63 Å20 Å2
2---1 Å20 Å2
3---2.014 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 96 109 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.89
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.34
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 35
RfactorNum. reflection% reflection
Rfree0.346 50 10.8 %
Rwork0.276 463 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACO_XPLOR_PAR.TXTACO_XPLOR_TOP.TXT
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.34

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