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- PDB-1e6i: Bromodomain from GCN5 complexed with acetylated H4 peptide -

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Basic information

Entry
Database: PDB / ID: 1e6i
TitleBromodomain from GCN5 complexed with acetylated H4 peptide
Components
  • HISTONE H4
  • TRANSCRIPTIONAL ACTIVATOR GCN5
KeywordsGENE REGULATION / HISTONE BINDING / N-ACETYL LYSINE
Function / homology
Function and homology information


ADA complex / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / histone crotonyltransferase activity / histone H3 acetyltransferase activity / SLIK (SAGA-like) complex / SUMOylation of chromatin organization proteins / replication fork protection complex ...ADA complex / HDMs demethylate histones / HATs acetylate histones / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / histone crotonyltransferase activity / histone H3 acetyltransferase activity / SLIK (SAGA-like) complex / SUMOylation of chromatin organization proteins / replication fork protection complex / RMTs methylate histone arginines / SAGA complex / peptide-lysine-N-acetyltransferase activity / Estrogen-dependent gene expression / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / chromosome, centromeric region / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold ...Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Bromodomain-like / Histone Acetyltransferase; Chain A / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H4 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.87 Å
AuthorsOwen, D.J. / Travers, A.A. / Evans, P.R.
CitationJournal: Embo J. / Year: 2000
Title: The Structural Basis for the Recognition of Acetylated Histone H4 by the Bromodomain of Histone Acetyltransferase Gcn5P
Authors: Owen, D.J. / Ornaghi, P. / Yang, J.C. / Lowe, N. / Evans, P.R. / Ballario, P. / Neuhaus, D. / Filetici, P. / Travers, A.A.
History
DepositionAug 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL ACTIVATOR GCN5
P: HISTONE H4


Theoretical massNumber of molelcules
Total (without water)16,2432
Polymers16,2432
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-4.5 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.680, 71.920, 89.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2094-

HOH

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Components

#1: Protein TRANSCRIPTIONAL ACTIVATOR GCN5


Mass: 14406.266 Da / Num. of mol.: 1 / Fragment: BROMODOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: GCN5 / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q03330
#2: Protein/peptide HISTONE H4 /


Mass: 1837.202 Da / Num. of mol.: 1 / Fragment: ACETYLATED TAIL, RESIDUES 16-30 / Source method: obtained synthetically / Details: LYSINE 16 IS ACETYLATED ON NZ / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02309
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHISTONE ACETYLTRANSFERASE (HAT) ACTION TO PROMOTE TRANSCRIPTIONAL ACTIVATION. BINDS PREFERENTIALLY ...HISTONE ACETYLTRANSFERASE (HAT) ACTION TO PROMOTE TRANSCRIPTIONAL ACTIVATION. BINDS PREFERENTIALLY TO LYSINE 14 OF H3 AND WITH A SOMEWHAT LOWER PREFERENCE TO LYSINES 8 AND 16 OF HISTONE H4.
Sequence detailsRESIDUES 319-324 (NOT VISIBLE) DERIVED FROM THE VECTOR K16 IS ACETYLATED

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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: 2.16 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5
Details: 2.2M AMMONIUM SULPHATE, 20% V/V GLYCEROL, 4MM DITHIOTHREITOL, 100 MM HEPES PH 7.5, 125MM NACL 5:1 PEPTIDE:PROTEIN
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMHEPES1drop
2250 mM1dropNaCl
31 mMdithiothreitol1drop
420 mg/mlprotein1drop
52.2 Mammonium sulfate1reservoir
620 %(v/v)glycerol1reservoir
74 mMdithiothreitol1reservoir
8100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 2000 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→19.1 Å / Num. obs: 88913 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 24.5
Reflection shellResolution: 1.87→1.98 Å / Redundancy: 7 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 8.7 / Rsym value: 0.204 / % possible all: 99.5
Reflection shell
*PLUS
% possible obs: 99.5 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.87→19 Å / SU B: 8 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.18 / Details: REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.209 572 4.8 %RANDOM
Rwork0.187 ---
obs-11944 99.8 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.87→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 0 109 1090
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.021
X-RAY DIFFRACTIONp_angle_d3.93
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.34
X-RAY DIFFRACTIONp_mcangle_it3.66
X-RAY DIFFRACTIONp_scbond_it3.45
X-RAY DIFFRACTIONp_scangle_it5.38
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.0940.2
X-RAY DIFFRACTIONp_singtor_nbd0.310.3
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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