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- PDB-7xay: Crystal structure of Hat1-Hat2-Asf1-H3-H4 -

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Basic information

Entry
Database: PDB / ID: 7xay
TitleCrystal structure of Hat1-Hat2-Asf1-H3-H4
Components
  • Histone H3
  • Histone H4
  • Histone acetyltransferase type B subunit 2
  • Histone chaperone asf1
  • Soluble cytochrome b562,Histone acetyltransferase type B catalytic subunit
KeywordsTRANSFERASE / Histone acetyltransferase / Histones / Enzymatic activity / Histone chaperone
Function / homology
Function and homology information


H3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / Rpd3L complex / Rpd3L-Expanded complex / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression ...H3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / Rpd3L complex / Rpd3L-Expanded complex / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / histone H4 acetyltransferase activity / DNA replication-dependent chromatin assembly / acetyltransferase activator activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / nucleosome disassembly / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / cellular response to stress / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / histone acetyltransferase complex / intracellular copper ion homeostasis / subtelomeric heterochromatin formation / histone acetyltransferase activity / histone acetyltransferase / CENP-A containing nucleosome / aerobic respiration / positive regulation of transcription elongation by RNA polymerase II / electron transport chain / protein modification process / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / chromatin organization / histone binding / periplasmic space / electron transfer activity / chromosome, telomeric region / chromatin remodeling / iron ion binding / protein heterodimerization activity / heme binding / chromatin binding / regulation of DNA-templated transcription / chromatin / DNA binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone ...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 deposition protein Asf1 / Histone chaperone ASF1-like / Histone chaperone ASF1-like superfamily / ASF1 like histone chaperone / Histone-binding protein RBBP4, N-terminal / Histone-binding protein RBBP4 or subunit C of CAF1 complex / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
COENZYME A / Histone H4 / Soluble cytochrome b562 / Histone acetyltransferase type B subunit 2 / Histone H3 / Histone acetyltransferase type B catalytic subunit / Histone chaperone asf1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Aspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsYue, Y. / Yang, W.S. / Xu, R.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91853204 China
CitationJournal: Genes Dev. / Year: 2022
Title: Topography of histone H3-H4 interaction with the Hat1-Hat2 acetyltransferase complex.
Authors: Yue, Y. / Yang, W.S. / Zhang, L. / Liu, C.P. / Xu, R.M.
History
DepositionMar 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble cytochrome b562,Histone acetyltransferase type B catalytic subunit
B: Histone acetyltransferase type B subunit 2
C: Histone chaperone asf1
D: Histone H3
E: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6096
Polymers136,8425
Non-polymers7681
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-68 kcal/mol
Surface area44330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.410, 124.684, 161.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 5 types, 5 molecules ABCDE

#1: Protein Soluble cytochrome b562,Histone acetyltransferase type B catalytic subunit / Cytochrome b-562


Mass: 48211.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: cybC, HAT1, YPL001W, LPA16W, YP8132.12 / Strain: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABE7, UniProt: Q12341, histone acetyltransferase
#2: Protein Histone acetyltransferase type B subunit 2


Mass: 45105.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HAT2, YEL056W / Production host: Escherichia coli (E. coli) / References: UniProt: P39984
#3: Protein Histone chaperone asf1 / Anti-silencing function protein 1


Mass: 17545.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: asf1, AFUA_3G11030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WXX5
#4: Protein Histone H3


Mass: 15259.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830
#5: Protein Histone H4


Mass: 10719.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: 3.54 Å3/Da / Density % sol: 70.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris propane, pH 6.5, 20% PEG-3350, and 200 mM sodium nitrate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→98.59 Å / Num. obs: 29577 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.48 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.4
Reflection shellResolution: 3.3→3.5 Å / Mean I/σ(I) obs: 3 / Num. unique obs: 4740 / CC1/2: 0.742

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PSW

4psw


Resolution: 3.3→22.4 Å / SU ML: 0.3833 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 1991 6.77 %
Rwork0.2304 27429 -
obs0.2321 29420 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.78 Å2
Refinement stepCycle: LAST / Resolution: 3.3→22.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8219 0 48 0 8267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038443
X-RAY DIFFRACTIONf_angle_d0.594611428
X-RAY DIFFRACTIONf_chiral_restr0.04461264
X-RAY DIFFRACTIONf_plane_restr0.00291460
X-RAY DIFFRACTIONf_dihedral_angle_d15.63873168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.380.34011400.30941939X-RAY DIFFRACTION99.76
3.38-3.470.34641430.30311952X-RAY DIFFRACTION99.81
3.47-3.580.29261430.27881970X-RAY DIFFRACTION99.72
3.58-3.690.30961400.26381925X-RAY DIFFRACTION99.57
3.69-3.820.30421400.27191938X-RAY DIFFRACTION99.19
3.82-3.970.29161410.26361934X-RAY DIFFRACTION99.43
3.97-4.150.29131430.25331971X-RAY DIFFRACTION99.11
4.15-4.370.26681420.23521950X-RAY DIFFRACTION99.29
4.37-4.640.24141410.21141947X-RAY DIFFRACTION98.91
4.64-50.22641420.20011953X-RAY DIFFRACTION98.82
5-5.490.25331440.20891974X-RAY DIFFRACTION98.79
5.49-6.270.24611400.23071948X-RAY DIFFRACTION96.94
6.27-7.840.20441460.22941994X-RAY DIFFRACTION98.35
7.85-22.40.21291460.18192034X-RAY DIFFRACTION96.25

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