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

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Basic information

Entry
Database: PDB / ID: 4psx
TitleCrystal structure of histone acetyltransferase complex
Components
  • (Histone acetyltransferase type B ...) x 2
  • Histone H3
  • Histone H4
KeywordsHISTONE/TRANSFERASE / HAT WD40 / acetyltransferase / AcCoA / Phosphorylation / HISTONE-TRANSFERASE complex
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Rpd3L complex / HDACs deacetylate histones / Rpd3L-Expanded complex / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / histone H4 acetyltransferase activity ...sexual sporulation resulting in formation of a cellular spore / HDMs demethylate histones / HATs acetylate histones / Rpd3L complex / HDACs deacetylate histones / Rpd3L-Expanded complex / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / histone H4 acetyltransferase activity / SUMOylation of chromatin organization proteins / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / subtelomeric heterochromatin formation / rRNA transcription / histone acetyltransferase complex / CENP-A containing nucleosome / histone acetyltransferase activity / histone acetyltransferase / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / DNA repair / 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 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / 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 H4 / Histone acetyltransferase type B subunit 2 / Histone H3 / Histone acetyltransferase type B catalytic subunit
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.509 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
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 type B catalytic subunit
B: Histone acetyltransferase type B subunit 2
C: Histone H4
D: Histone acetyltransferase type B catalytic subunit
E: Histone acetyltransferase type B subunit 2
F: Histone H4
Y: Histone H3
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,29711
Polymers178,6668
Non-polymers1,6313
Water10,917606
1
A: Histone acetyltransferase type B catalytic subunit
B: Histone acetyltransferase type B subunit 2
C: Histone H4
Y: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1976
Polymers89,3334
Non-polymers8642
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-29 kcal/mol
Surface area32150 Å2
MethodPISA
2
D: Histone acetyltransferase type B catalytic subunit
E: Histone acetyltransferase type B subunit 2
F: Histone H4
P: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1015
Polymers89,3334
Non-polymers7681
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-10 kcal/mol
Surface area31200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.548, 85.331, 114.510
Angle α, β, γ (deg.)75.97, 72.40, 66.06
Int Tables number1
Space group name H-MP1

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Components

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Histone acetyltransferase type B ... , 2 types, 4 molecules ADBE

#1: Protein Histone acetyltransferase type B catalytic subunit


Mass: 37566.344 Da / Num. of mol.: 2 / Fragment: UNP residues 7-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HAT1, LPA16W, YP8132.12, YPL001W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12341, histone acetyltransferase
#2: Protein Histone acetyltransferase type B subunit 2


Mass: 45107.902 Da / Num. of mol.: 2 / Fragment: UNP residues 8-389 / Mutation: V143T
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

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Protein/peptide , 2 types, 4 molecules CFYP

#3: Protein/peptide Histone H4 /


Mass: 5093.079 Da / Num. of mol.: 2 / Fragment: UNP residues 2-49 / Mutation: I21V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309
#4: Protein/peptide Histone H3 /


Mass: 1565.797 Da / Num. of mol.: 2 / Fragment: UNP residues 2-16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61830

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Non-polymers , 3 types, 609 molecules

#5: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / 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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M potassium sodium tartrate, 20%(w/v) polyethylene glycol 3,350, 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: 2.5→38.6 Å / Num. all: 66418 / Num. obs: 66418 / % possible obs: 75.67 % / Observed criterion σ(F): 1.98 / Observed criterion σ(I): 1.98
Reflection shellResolution: 2.5→2.55 Å / % possible all: 75.67

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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
Starting model: 4PSW

4psw


Resolution: 2.509→38.6 Å / SU ML: 0.23 / σ(F): 1.98 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 3338 5.03 %
Rwork0.1807 --
obs0.1829 66417 75.67 %
all-66418 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.509→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11685 0 101 606 12392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912053
X-RAY DIFFRACTIONf_angle_d1.25216333
X-RAY DIFFRACTIONf_dihedral_angle_d15.8814465
X-RAY DIFFRACTIONf_chiral_restr0.081776
X-RAY DIFFRACTIONf_plane_restr0.0062092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5092-2.5450.3577110.238234110
2.545-2.5830.3348320.24552616
2.583-2.62340.3211460.239685024
2.6234-2.66640.2214580.2505110832
2.6664-2.71230.2826540.2393146341
2.7123-2.76170.28621050.2578169350
2.7617-2.81480.2811220.257207860
2.8148-2.87220.26661380.2352230867
2.8722-2.93460.2791190.2324264376
2.9346-3.00290.29651630.2334284882
3.0029-3.07790.26071590.2252309589
3.0779-3.16110.24111680.215328394
3.1611-3.25410.2651800.2098335897
3.2541-3.35910.25061770.1916342898
3.3591-3.4790.2381750.1838340998
3.479-3.61820.21671750.1662341098
3.6182-3.78280.22511740.159343298
3.7828-3.9820.20621740.1587340198
3.982-4.23120.18871940.1506343598
4.2312-4.55750.16621710.1368340698
4.5575-5.01520.17292070.138337098
5.0152-5.73890.19461810.157338097
5.7389-7.22270.22231880.1935335797
7.2227-38.63030.21521670.1772345799
Refinement TLS params.Method: refined / Origin x: -13.3471 Å / Origin y: -60.3416 Å / Origin z: -15.4922 Å
111213212223313233
T0.4191 Å2-0.0133 Å2-0.0014 Å2-0.345 Å20.101 Å2--0.4127 Å2
L0.5823 °2-0.0182 °2-0.0246 °2--0.0297 °20.0443 °2--0.5701 °2
S0.0647 Å °0.0001 Å °0.0192 Å °0.0001 Å °0.0004 Å °-0.0446 Å °-0.0146 Å °0.0196 Å °-0.0528 Å °
Refinement TLS groupSelection details: all

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