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- PDB-6vo5: Crystal structure of Human histone acetytransferas 1 (HAT1) in co... -

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Basic information

Entry
Database: PDB / ID: 6vo5
TitleCrystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4
Components
  • Histone H4
  • Histone acetyltransferase type B catalytic subunit
KeywordsTRANSFERASE / HAT1 / histone acetyltransferase 1 / Isobutyryl-CoA / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H4K12 acetyltransferase activity / histone H4 acetyltransferase activity / internal protein amino acid acetylation / subtelomeric heterochromatin formation / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends ...histone H4K12 acetyltransferase activity / histone H4 acetyltransferase activity / internal protein amino acid acetylation / subtelomeric heterochromatin formation / chromosome organization / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / histone acetyltransferase activity / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / histone acetyltransferase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nuclear matrix / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / chromatin / protein-containing complex / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
: / Histone acetyltransferase type B catalytic subunit, 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 / Acyl-CoA N-acyltransferase / Histone H4, conserved site / Histone H4 signature. ...: / Histone acetyltransferase type B catalytic subunit, 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 / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold
Similarity search - Domain/homology
ACETATE ION / ISOBUTYRYL-COENZYME A / Histone acetyltransferase type B catalytic subunit / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsHalabelian, L. / Zeng, H. / Dong, A. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4
Authors: Halabelian, L. / Zeng, H. / Dong, A. / Loppnau, P. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionJan 30, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionMar 11, 2020ID: 6UHD
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,36828
Polymers80,1654
Non-polymers2,20324
Water13,241735
1
A: Histone acetyltransferase type B catalytic subunit
C: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,16715
Polymers40,0832
Non-polymers1,08513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-22 kcal/mol
Surface area16780 Å2
MethodPISA
2
B: Histone acetyltransferase type B catalytic subunit
D: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20013
Polymers40,0832
Non-polymers1,11811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-17 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.726, 155.636, 53.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Histone acetyltransferase type B catalytic subunit / Histone acetyltransferase 1


Mass: 38139.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAT1, KAT1 / Plasmid: pET28a-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pRARE2 / References: UniProt: O14929, histone acetyltransferase
#2: Protein/peptide Histone H4 /


Mass: 1943.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805

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Non-polymers , 6 types, 759 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CO6 / ISOBUTYRYL-COENZYME A / IB-CO6 / Isobutyryl-CoA


Mass: 837.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H42N7O17P3S / Comment: antibiotic*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 16 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% PEG 20K and 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.6→48.62 Å / Num. obs: 128467 / % possible obs: 99.5 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.021 / Rrim(I) all: 0.062 / Net I/σ(I): 20.3 / Num. measured all: 1132308 / Scaling rejects: 89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.639.11.0665763463220.7230.3671.1291.999.5
8.76-48.628.20.02574359030.9990.0090.02766.998.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→47.45 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.621 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 6413 5 %RANDOM
Rwork0.1708 ---
obs0.1721 121983 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.12 Å2 / Biso mean: 25.604 Å2 / Biso min: 14.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2--0 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: final / Resolution: 1.6→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 160 746 6356
Biso mean--38.59 37.68 -
Num. residues----669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175320
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.668064
X-RAY DIFFRACTIONr_angle_other_deg1.3641.57612327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1721.541331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38215974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4141543
X-RAY DIFFRACTIONr_chiral_restr0.070.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021368
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 471 -
Rwork0.255 8941 -
all-9412 -
obs--99.5 %

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