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- PDB-5j8f: Human MOF K274P crystal structure -

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Basic information

Entry
Database: PDB / ID: 5j8f
TitleHuman MOF K274P crystal structure
ComponentsHistone acetyltransferase KAT8
KeywordsTRANSFERASE / acetyltransferase / MYST / GNAT / epigenetics
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / MSL complex / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / MSL complex / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation / post-embryonic hemopoiesis / negative regulation of epithelial to mesenchymal transition / NSL complex / peptide-lysine-N-acetyltransferase activity / oogenesis / NuA4 histone acetyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / regulation of autophagy / transcription coregulator activity / kinetochore / nuclear matrix / chromosome / HATs acetylate histones / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
N-acetyl transferase-like / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain ...N-acetyl transferase-like / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMcCullough, C.E. / Marmorstein, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)5P01AG031862-08 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Functional Role of Acetyltransferase hMOF K274 Autoacetylation.
Authors: McCullough, C.E. / Song, S. / Shin, M.H. / Johnson, F.B. / Marmorstein, R.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2024
Polymers36,0651
Non-polymers1363
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.094, 55.846, 122.405
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 KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 36065.430 Da / Num. of mol.: 1 / Fragment: UNP residues 177-458 / Mutation: K274P
Source method: isolated from a genetically manipulated source
Details: Missing residues were not modeled due to lack of density
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Plasmid: PRSFDuet
Details (production host): Protein generative with TEV cleavable His tag
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9H7Z6, histone acetyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.19 Å3/Da / Density % sol: 43.77 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.28M Ammonium Chloride 26%PEG 3350 0.1M BisTris-HCl pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03315 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2015 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.6→41.253 Å / Num. obs: 10295 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 42.491 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 18.05
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8C

5j8c


Resolution: 2.6→41.253 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1024 10 %Random selection
Rwork0.2391 ---
obs0.2428 10236 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 3 19 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062097
X-RAY DIFFRACTIONf_angle_d0.912856
X-RAY DIFFRACTIONf_dihedral_angle_d21.992721
X-RAY DIFFRACTIONf_chiral_restr0.051307
X-RAY DIFFRACTIONf_plane_restr0.007356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5979-2.73490.38871410.3081269X-RAY DIFFRACTION99
2.7349-2.90620.31951440.3021298X-RAY DIFFRACTION100
2.9062-3.13050.33631430.29071291X-RAY DIFFRACTION100
3.1305-3.44540.32661450.25951301X-RAY DIFFRACTION100
3.4454-3.94360.25921470.2251314X-RAY DIFFRACTION100
3.9436-4.96720.21221470.19951329X-RAY DIFFRACTION100
4.9672-41.25820.25841570.22151410X-RAY DIFFRACTION100

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