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- PDB-5j8c: Human MOF C316S, E350Q crystal structure -

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Basic information

Entry
Database: PDB / ID: 5j8c
TitleHuman MOF C316S, E350Q 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 / MSL complex / protein propionyltransferase activity / histone H4 acetyltransferase activity / regulation of mRNA processing / dosage compensation by inactivation of X chromosome / myeloid cell differentiation / post-embryonic hemopoiesis / NSL complex ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / protein propionyltransferase activity / histone H4 acetyltransferase activity / regulation of mRNA processing / dosage compensation by inactivation of X chromosome / myeloid cell differentiation / post-embryonic hemopoiesis / NSL complex / negative regulation of epithelial to mesenchymal transition / protein-lysine-acetyltransferase activity / negative regulation of type I interferon production / oogenesis / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / positive regulation of transcription initiation by RNA polymerase II / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / nuclear matrix / HATs acetylate histones / chromosome / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of autophagy / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / zinc ion binding / nucleoplasm / nucleus
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 ...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: 2.17 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 ...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_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)36,3046
Polymers36,1211
Non-polymers1825
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.148, 55.676, 122.311
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: 36121.477 Da / Num. of mol.: 1 / Fragment: UNP residues 177-458 / Mutation: C316S E350Q
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.12 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium Chloride 28% 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: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 27, 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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.17→27.838 Å / Num. obs: 17414 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.3
Reflection shellResolution: 2.17→2.2 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.2 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QAH

3qah


Resolution: 2.17→27.838 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2337 1732 9.97 %Random selection
Rwork0.1905 ---
obs0.1949 17414 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.13 Å2
Refinement stepCycle: LAST / Resolution: 2.17→27.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 5 77 2250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082234
X-RAY DIFFRACTIONf_angle_d0.8913036
X-RAY DIFFRACTIONf_dihedral_angle_d14.8871306
X-RAY DIFFRACTIONf_chiral_restr0.053324
X-RAY DIFFRACTIONf_plane_restr0.006377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.166-2.19830.26091410.26631233X-RAY DIFFRACTION93
2.1983-2.23260.27011370.25771214X-RAY DIFFRACTION100
2.2326-2.26920.28111420.23861268X-RAY DIFFRACTION100
2.2692-2.30830.33781430.24331287X-RAY DIFFRACTION100
2.3083-2.35030.29111370.24911244X-RAY DIFFRACTION100
2.3503-2.39550.26881420.23151273X-RAY DIFFRACTION100
2.3955-2.44430.29521390.24231259X-RAY DIFFRACTION100
2.4443-2.49750.26561400.2171265X-RAY DIFFRACTION100
2.4975-2.55550.27331400.21461273X-RAY DIFFRACTION100
2.5555-2.61940.22661410.2111243X-RAY DIFFRACTION100
2.6194-2.69010.25141410.20911279X-RAY DIFFRACTION100
2.6901-2.76920.32071380.21061261X-RAY DIFFRACTION100
2.7692-2.85850.28241410.20591262X-RAY DIFFRACTION100
2.8585-2.96060.22591410.1951268X-RAY DIFFRACTION100
2.9606-3.0790.28511350.19841274X-RAY DIFFRACTION100
3.079-3.21890.2141330.1851249X-RAY DIFFRACTION99
3.2189-3.38840.2331400.18281251X-RAY DIFFRACTION99
3.3884-3.60020.24691360.17761278X-RAY DIFFRACTION100
3.6002-3.87750.2331440.16821252X-RAY DIFFRACTION99
3.8775-4.26650.20361410.15851270X-RAY DIFFRACTION99
4.2665-4.8810.19781390.15641243X-RAY DIFFRACTION99
4.881-6.13870.1951370.19071273X-RAY DIFFRACTION100
6.1387-27.84030.19791420.18611256X-RAY DIFFRACTION99

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