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- PDB-4psw: Crystal structure of histone acetyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 4psw
TitleCrystal structure of histone acetyltransferase complex
Components
  • Histone H4 type VIII
  • Histone acetyltransferase type B catalytic subunit
  • Histone acetyltransferase type B subunit 2
KeywordsTRANSFERASE / HAT WD40 / histone acetyltransferase / AcCoA / Phosphorylation / Cytoplasmatic
Function / homology
Function and homology information


HATs acetylate histones / Rpd3L complex / HDACs deacetylate histones / Rpd3L-Expanded complex / histone H4 acetyltransferase activity / subtelomeric heterochromatin formation / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / DNA-templated transcription initiation ...HATs acetylate histones / Rpd3L complex / HDACs deacetylate histones / Rpd3L-Expanded complex / histone H4 acetyltransferase activity / subtelomeric heterochromatin formation / histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / DNA-templated transcription initiation / nucleosome / chromatin organization / histone binding / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / DNA repair / host cell nucleus / chromatin binding / regulation of DNA-templated transcription / DNA binding / nucleus / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #390 / Histone Acetyltransferase; domain 1 / Histone acetyl transferase 1 (HAT1), N-terminal domain / Fungal HAT1, C-terminal / Histone acetyltransferase HAT1, C-terminal / Histone acetyltransferase type B, catalytic subunit / Histone acetyl transferase HAT1 N-terminal / Histone acetyl transferase 1, N-terminal domain superfamily / Histone acetyl transferase HAT1 N-terminus / Histone-binding protein RBBP4, N-terminal ...Arc Repressor Mutant, subunit A - #390 / Histone Acetyltransferase; domain 1 / Histone acetyl transferase 1 (HAT1), N-terminal domain / Fungal HAT1, C-terminal / Histone acetyltransferase HAT1, C-terminal / Histone acetyltransferase type B, catalytic subunit / Histone acetyl transferase HAT1 N-terminal / Histone acetyl transferase 1, N-terminal domain superfamily / Histone acetyl transferase HAT1 N-terminus / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / GNAT domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Acyl-CoA N-acyltransferase / Aminopeptidase / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Arc Repressor Mutant, subunit A / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Histone acetyltransferase type B subunit 2 / Histone acetyltransferase type B catalytic subunit / Histone H4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Ophiophagus hannah (king cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsYang, M. / Li, Y.
CitationJournal: Genes Dev. / Year: 2014
Title: Hat2p recognizes the histone H3 tail to specify the acetylation of the newly synthesized H3/H4 heterodimer by the Hat1p/Hat2p complex
Authors: Li, Y. / Zhang, L. / Liu, T. / Chai, C. / Fang, Q. / Wu, H. / Agudelo garcia, P.A. / Han, Z. / Zong, S. / Yu, Y. / Zhang, X. / Parthun, M.R. / Chai, J. / Xu, R.M. / Yang, M.
History
DepositionMar 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase type B catalytic subunit
B: Histone acetyltransferase type B subunit 2
C: Histone H4 type VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3664
Polymers86,5993
Non-polymers7681
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-11 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.986, 98.441, 124.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone acetyltransferase type B catalytic subunit


Mass: 37276.992 Da / Num. of mol.: 1 / Fragment: UNP residues 4-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HAT1, YPL001W, LPA16W, YP8132.12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12341, histone acetyltransferase
#2: Protein Histone acetyltransferase type B subunit 2


Mass: 45187.879 Da / Num. of mol.: 1 / Fragment: UNP residues 7-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HAT2, YEL056W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P39984
#3: Protein/peptide Histone H4 type VIII


Mass: 4133.991 Da / Num. of mol.: 1 / Fragment: UNP residues 8-45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiophagus hannah (king cobra) / Gene: H4-VIII, L345_01081 / Production host: Escherichia coli (E. coli) / References: UniProt: V8PGJ1
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M potassium sodium tartrate and 20%(w/v) polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→29.7 Å / Num. all: 56511 / Num. obs: 56511 / % possible obs: 99.8 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34
Reflection shellResolution: 2.1→29.7 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→29.7 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 2868 5.08 %
Rwork0.1705 --
obs0.1726 56511 99.77 %
all-56511 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 48 526 6398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096010
X-RAY DIFFRACTIONf_angle_d1.1888148
X-RAY DIFFRACTIONf_dihedral_angle_d16.3692227
X-RAY DIFFRACTIONf_chiral_restr0.084882
X-RAY DIFFRACTIONf_plane_restr0.0051044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1370.28261390.22322595X-RAY DIFFRACTION99
2.137-2.17590.25411480.2052633X-RAY DIFFRACTION100
2.1759-2.21770.28911330.21292666X-RAY DIFFRACTION100
2.2177-2.2630.26431230.20332664X-RAY DIFFRACTION100
2.263-2.31220.25881450.20842654X-RAY DIFFRACTION100
2.3122-2.36590.25131490.19542676X-RAY DIFFRACTION100
2.3659-2.42510.28051240.19182669X-RAY DIFFRACTION100
2.4251-2.49060.24851290.1882658X-RAY DIFFRACTION100
2.4906-2.56380.23711530.18982685X-RAY DIFFRACTION100
2.5638-2.64650.20761600.1852631X-RAY DIFFRACTION100
2.6465-2.74110.26831410.18882671X-RAY DIFFRACTION100
2.7411-2.85070.2371530.1752668X-RAY DIFFRACTION100
2.8507-2.98040.20361520.17582686X-RAY DIFFRACTION100
2.9804-3.13730.20091480.17472672X-RAY DIFFRACTION100
3.1373-3.33370.2041520.16682677X-RAY DIFFRACTION100
3.3337-3.59060.17451430.15732714X-RAY DIFFRACTION100
3.5906-3.95120.20181500.14812682X-RAY DIFFRACTION99
3.9512-4.52130.18921390.13862714X-RAY DIFFRACTION99
4.5213-5.68980.16761400.14342767X-RAY DIFFRACTION100
5.6898-29.73560.19541470.1722861X-RAY DIFFRACTION99
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)
11.18030.6443-0.4031.0725-0.66270.988-0.13680.1912-0.1913-0.28610.0362-0.14660.087-0.01890.08630.32210.00420.05360.1837-0.06550.225-3.4814-37.551511.0169
21.2328-0.1405-0.05580.69310.11741.2050.02370.06240.1095-0.0864-0.0094-0.0396-0.0859-0.0422-0.02120.0922-0.02320.01030.11880.01490.1459-22.0797-23.014948.5177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:320 )A5 - 320
2X-RAY DIFFRACTION2( CHAIN B AND RESID 7:390 )B7 - 390

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