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Open data
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Basic information
Entry | Database: PDB / ID: 3gg3 | ||||||
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Title | Crystal Structure of the Bromodomain of Human PCAF | ||||||
![]() | Histone acetyltransferase PCAF | ||||||
![]() | TRANSFERASE / PCAF / K(lysine) acetyltransferase 2B / KAT2B / GCN5 / GCN5L / P / P/CAF / CREBBP-associated factor / p300/CBP-associated factor / SGC / Structural Genomics Consortium / Acyltransferase / Bromodomain / Cell cycle / Host-virus interaction / Nucleus / Phosphoprotein / Transcription / Transcription regulation | ||||||
Function / homology | ![]() regulation of protein ADP-ribosylation / negative regulation of rRNA processing / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / positive regulation of transcription from RNA polymerase II promoter by glucose / diamine N-acetyltransferase activity / 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 / positive regulation of transcription from RNA polymerase II promoter by glucose / diamine N-acetyltransferase activity / 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 / 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 / cellular response to parathyroid hormone stimulus / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / SAGA complex / limb development / Regulation of FOXO transcriptional activity by acetylation / NOTCH4 Intracellular Domain Regulates Transcription / A band / NOTCH3 Intracellular Domain Regulates Transcription / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / histone acetyltransferase binding / protein acetylation / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / Formation of paraxial mesoderm / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of RNA splicing / regulation of embryonic development / acetyltransferase activity / regulation of DNA repair / histone acetyltransferase activity / 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 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / mitotic spindle / memory / kinetochore / 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 / histone deacetylase binding / vasodilation / cellular response to insulin stimulus / 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 / 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Filippakopoulos, P. / Keates, T. / Picaud, S. / Rehana, K. / Fedorov, O. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Keates, T. / Picaud, S. / Rehana, K. / Fedorov, O. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Histone recognition and large-scale structural analysis of the human bromodomain family. Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.9 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.5 KB | Display | ![]() |
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Full document | ![]() | 436.1 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nxbSC ![]() 2oo1SC ![]() 2ossSC ![]() 2ouoSC ![]() 2rfjSC ![]() 3d7cC ![]() 3daiSC ![]() 3dwyC ![]() 3hmeC ![]() 3hmfC ![]() 3hmhC ![]() 3i3jC ![]() 3iu5C ![]() 3iu6C ![]() 3lxjC ![]() 3mb3C ![]() 3mb4C ![]() 3mqmC ![]() 3nxbC ![]() 3p1cC ![]() 3p1dC ![]() 3q2eC ![]() 3rcwC ![]() 3tlpC ![]() 3uv2C ![]() 3uv4C ![]() 3uv5C ![]() 3uvdC ![]() 3uvwC ![]() 3uvxC ![]() 3uvyC ![]() 3uw9C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 726 - 828 / Label seq-ID: 14 - 116
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Components
#1: Protein | Mass: 14172.371 Da / Num. of mol.: 2 / Fragment: UNP residues 715-831 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 20% PEG10K, 4% Ethylene Glycol, 0.1M HEPES pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 13, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→32.743 Å / Num. all: 17604 / Num. obs: 17604 / % possible obs: 100 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2 / Num. unique all: 2567 / Rsym value: 0.456 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 51.03 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI Resolution: 2.25→32.74 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.206 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.855 / SU B: 9.935 / SU ML: 0.129 / SU R Cruickshank DPI: 0.214 / SU Rfree: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.81 Å2 / Biso mean: 31.265 Å2 / Biso min: 7.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→32.74 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1380 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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