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- PDB-2pq8: MYST histone acetyltransferase 1 -

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Basic information

Entry
Database: PDB / ID: 2pq8
TitleMYST histone acetyltransferase 1
ComponentsProbable histone acetyltransferase MYST1
KeywordsTRANSFERASE / myst / mof / HISTONE ACETYLTRANSFERASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / 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 / MSL complex / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / protein propionyltransferase activity / regulation of mRNA processing / histone H4 acetyltransferase activity / myeloid cell differentiation / post-embryonic hemopoiesis / NSL complex / negative regulation of epithelial to mesenchymal transition / peptide-lysine-N-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 acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neurogenesis / transcription initiation-coupled chromatin remodeling / 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 / chromatin / 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 ...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
COENZYME A / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsTempel, W. / Wu, H. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: MYST histone acetyltransferase 1.
Authors: Wu, H. / Tempel, W. / Dombrovski, L. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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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)33,38916
Polymers32,5571
Non-polymers83315
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.060, 64.172, 93.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsnot known

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Components

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


Mass: 32556.520 Da / Num. of mol.: 1 / Fragment: Residues 174-449 / Mutation: K274R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYST1, MOF, PP7073 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.3 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 24% PEG3350, 0.2 M Ammonium chloride, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 49643 / % possible obs: 99.5 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.047 / Χ2: 1.179 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
1.45-1.59750.59447490.74
1.5-1.5699.75.80.43948920.76
1.56-1.631006.20.29749270.761
1.63-1.7299.96.40.21449400.808
1.72-1.831006.60.14649460.886
1.83-1.971006.70.09949351.111
1.97-2.171006.90.06649761.358
2.17-2.4810070.0550161.528
2.48-3.1210070.03750411.61
3.12-5098.86.60.02852211.865

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.22 Å
Translation2.5 Å29.22 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GIV

2giv


Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.203 / SU B: 1.173 / SU ML: 0.047 / ESU R: 0.075 / ESU R Free: 0.076
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Prodrg, ARP/wARP, Molprobity, COOT programs have also been used in refinement. Acetyl coenzyme A was added to the protein sample. However, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Prodrg, ARP/wARP, Molprobity, COOT programs have also been used in refinement. Acetyl coenzyme A was added to the protein sample. However, electron density suggests the presence of de-acetylated coenzyme A bound to a reducing agent such as beta-mercaptoethanol that was also present in the protein sample.
RfactorNum. reflection% reflection
Rfree0.2308 2536 5.116 %
Rwork0.2049 --
all0.206 --
obs-49566 99.49 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.276 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.351 Å20 Å2
3----0.431 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 62 149 2334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222243
X-RAY DIFFRACTIONr_bond_other_d0.0020.021490
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9793069
X-RAY DIFFRACTIONr_angle_other_deg0.8653.0023623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0065269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52424.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68715360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.129155
X-RAY DIFFRACTIONr_chiral_restr0.0920.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_nbd_refined0.2130.2429
X-RAY DIFFRACTIONr_nbd_other0.1870.21470
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21095
X-RAY DIFFRACTIONr_nbtor_other0.0860.21072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2122
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.212
X-RAY DIFFRACTIONr_mcbond_it1.92721356
X-RAY DIFFRACTIONr_mcbond_other0.5372522
X-RAY DIFFRACTIONr_mcangle_it2.63632141
X-RAY DIFFRACTIONr_scbond_it2.42321058
X-RAY DIFFRACTIONr_scangle_it3.2393922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.45-1.4880.3611890.30332950.306363995.741
1.488-1.5280.2741570.25233590.253353899.378
1.528-1.5730.2451910.23832300.239342699.854
1.573-1.6210.2372040.21231300.214333599.97
1.621-1.6740.2531610.2130740.212323999.877
1.674-1.7320.2671580.19629920.199315199.968
1.732-1.7980.2411380.20329220.205306199.967
1.798-1.8710.2131340.20227610.202289699.965
1.871-1.9540.2061240.19926900.1992814100
1.954-2.0480.2051090.18925680.1892677100
2.048-2.1590.2281310.19324510.195258399.961
2.159-2.2890.1991440.1922950.1912439100
2.289-2.4460.2241200.19921890.2231199.913
2.446-2.640.2481160.20120210.2032137100
2.64-2.890.247930.21119020.2121995100
2.89-3.2280.2391130.20516900.207180499.945
3.228-3.720.203940.19915150.21609100
3.72-4.5380.226770.17413060.177138999.568
4.538-6.3460.216550.21810400.218109999.636
6.346-300.298280.2636000.26567892.625

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