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- PDB-3qah: Crystal structure of apo-form human MOF catalytic domain -

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Basic information

Entry
Database: PDB / ID: 3qah
TitleCrystal structure of apo-form human MOF catalytic domain
ComponentsProbable histone acetyltransferase MYST1
KeywordsTRANSFERASE / human MOF / MYST / histone acetyltransferase / dosage compensation / autoacetylation / H4K16 acetylation
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 / 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 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: 2.1 Å
AuthorsSun, B. / Tang, Q. / Zhong, C. / Ding, J.
CitationJournal: Cell Res. / Year: 2011
Title: Regulation of the histone acetyltransferase activity of hMOF via autoacetylation of Lys274
Authors: Sun, B. / Guo, S. / Tang, Q. / Li, C. / Zeng, R. / Xiong, Z. / Zhong, C. / Ding, J.
History
DepositionJan 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 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: Probable histone acetyltransferase MYST1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7842
Polymers35,7191
Non-polymers651
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.913, 60.690, 124.368
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable histone acetyltransferase MYST1 / MYST-1 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 35718.922 Da / Num. of mol.: 1
Fragment: apo-form human MOF catalytic domain, UNP residues 174-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOF, MYST1, PP7073 / Plasmid: PSJ2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 0.2M MgCl2, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20135 / % possible obs: 95.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0070refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GIV

2giv


Resolution: 2.1→43.07 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.36 / SU B: 9.859 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 1022 5.1 %RANDOM
Rwork0.1932 ---
obs0.195 20086 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.56 Å2 / Biso mean: 27.1207 Å2 / Biso min: 2.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2--2.24 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2266 0 1 194 2461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222332
X-RAY DIFFRACTIONr_angle_refined_deg0.991.9683156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2465271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65723.981103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.123158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211746
X-RAY DIFFRACTIONr_mcbond_it1.7951.51368
X-RAY DIFFRACTIONr_mcangle_it2.99322223
X-RAY DIFFRACTIONr_scbond_it3.5433964
X-RAY DIFFRACTIONr_scangle_it5.714.5933
X-RAY DIFFRACTIONr_rigid_bond_restr2.64232332
X-RAY DIFFRACTIONr_sphericity_free2.293195
X-RAY DIFFRACTIONr_sphericity_bonded0.94832266
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 55 -
Rwork0.229 1169 -
all-1224 -
obs--81.44 %

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