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- PDB-3tob: Human MOF E350Q crystal structure with active site lysine partial... -

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Basic information

Entry
Database: PDB / ID: 3tob
TitleHuman MOF E350Q crystal structure with active site lysine partially acetylated
Componentshistone acetyltransferase MYST1
KeywordsTRANSFERASE / MYST protein / HAT domain / zinc finger
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: 2.703 Å
AuthorsYuan, H. / Ding, E.C. / Marmorstein, R.
CitationJournal: Embo J. / Year: 2011
Title: MYST protein acetyltransferase activity requires active site lysine autoacetylation.
Authors: Yuan, H. / Rossetto, D. / Mellert, H. / Dang, W. / Srinivasan, M. / Johnson, J. / Hodawadekar, S. / Ding, E.C. / Speicher, K. / Abshiru, N. / Perry, R. / Wu, J. / Yang, C. / Zheng, Y.G. / ...Authors: Yuan, H. / Rossetto, D. / Mellert, H. / Dang, W. / Srinivasan, M. / Johnson, J. / Hodawadekar, S. / Ding, E.C. / Speicher, K. / Abshiru, N. / Perry, R. / Wu, J. / Yang, C. / Zheng, Y.G. / Speicher, D.W. / Thibault, P. / Verreault, A. / Johnson, F.B. / Berger, S.L. / Sternglanz, R. / McMahon, S.B. / Cote, J. / Marmorstein, R.
History
DepositionSep 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 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 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histone acetyltransferase MYST1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8763
Polymers35,7751
Non-polymers1012
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.971, 58.042, 120.338
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 MYST1 / MYST-1 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / hMOF


Mass: 35775.137 Da / Num. of mol.: 1 / Fragment: UNP residues 177-447 / Mutation: E350Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYST1, MOF, PP7073 / Production host: Escherichia coli (E. coli) / 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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE LYS 274 IS PARTIALLY ACETYLATED.

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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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 12662 / Num. obs: 12662 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.4
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 6.6 / Num. unique all: 614 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GIV

2giv


Resolution: 2.703→34.522 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 23.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 442 4.75 %RANDOM
Rwork0.2034 ---
all0.2057 9296 --
obs0.2057 9296 99.84 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.73 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8971 Å20 Å20 Å2
2--5.7981 Å2-0 Å2
3---1.099 Å2
Refinement stepCycle: LAST / Resolution: 2.703→34.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 2 31 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092300
X-RAY DIFFRACTIONf_angle_d1.1763124
X-RAY DIFFRACTIONf_dihedral_angle_d16.074842
X-RAY DIFFRACTIONf_chiral_restr0.078331
X-RAY DIFFRACTIONf_plane_restr0.005391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.703-3.09330.36011510.27092879X-RAY DIFFRACTION100
3.0933-3.89640.25771490.19542917X-RAY DIFFRACTION100
3.8964-34.52510.20511420.18443058X-RAY DIFFRACTION100

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