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- PDB-2rc4: Crystal Structure of the HAT domain of the human MOZ protein -

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Basic information

Entry
Database: PDB / ID: 2rc4
TitleCrystal Structure of the HAT domain of the human MOZ protein
ComponentsHistone acetyltransferase MYST3
KeywordsTRANSFERASE / Coenzyme A binding domain / zinc-finger / helix-turn-helix / Activator / Acyltransferase / Chromatin regulator / Metal-binding / Nucleus / Phosphorylation / Proto-oncogene / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex ...histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / protein acetylation / acetyltransferase activity / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / regulation of signal transduction by p53 class mediator / transcription coregulator activity / PML body / nucleosome / cellular senescence / nucleosome assembly / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
N-acetyl transferase-like / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 ...N-acetyl transferase-like / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Gcn5-related N-acetyltransferase (GNAT) / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Aminopeptidase / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Arc Repressor Mutant, subunit A / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsHolbert, M.A. / Sikorski, T. / Snowflack, D. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The human monocytic leukemia zinc finger histone acetyltransferase domain contains DNA-binding activity implicated in chromatin targeting.
Authors: Holbert, M.A. / Sikorski, T. / Carten, J. / Snowflack, D. / Hodawadekar, S. / Marmorstein, R.
History
DepositionSep 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase MYST3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8973
Polymers34,0221
Non-polymers8752
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.200, 109.200, 144.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Histone acetyltransferase MYST3 / MYST protein 3 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / Runt-related transcription factor- ...MYST protein 3 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / Runt-related transcription factor-binding protein 2 / Monocytic leukemia zinc finger protein / Zinc finger protein 220


Mass: 34021.637 Da / Num. of mol.: 1 / Fragment: HAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYST3, MOZ, RUNXBP2, ZNF220 / Production host: Escherichia coli (E. coli)
References: UniProt: Q92794, histone acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: sodium cacodylate, PEG 3350, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9795, 1.2571, 1.2829, 1.2832
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.25711
31.28291
41.28321
ReflectionAv σ(I) over netI: 11.7 / Number: 98811 / Rmerge(I) obs: 0.063 / Χ2: 0.99 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 13795 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.895099.210.0250.876
5.476.8910010.0411.062
4.785.4710010.0450.967
4.344.7810010.0470.955
4.034.3410010.0660.971
3.794.0310010.1090.996
3.63.7910010.1551.057
3.453.610010.2230.997
3.313.4510010.3271.006
3.23.3110010.4581.075
ReflectionResolution: 2.67→50 Å / Num. obs: 12178 / % possible obs: 95.2 % / Rmerge(I) obs: 0.082 / Χ2: 1.05 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.67-2.770.0727780.9911,262.3
2.77-2.880.65411850.9531,294.3
2.88-3.010.47912480.9681,299.9
3.01-3.170.26912501.0741,2100
3.17-3.360.15112651.0841,2100
3.36-3.620.10812701.0481,2100
3.62-3.990.0812751.0921,2100
3.99-4.560.06612951.0021,2100
4.56-5.750.06612971.0911,299.8
5.75-500.06713151.0961,294.7

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3.5 Å / D res low: 20 Å / FOM : 0.56 / Reflection: 5682
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength11.284.76-2.55
13 wavelength21.28363.41-8.83
13 wavelength31.28325.91-10.45
Phasing MAD set siteAtom type symbol: Zn / B iso: 60 / Fract x: 0.119 / Fract y: 0.407 / Fract z: 0.058 / Occupancy: 0.684
Phasing MAD shell
Resolution (Å)FOM Reflection
11.16-200.63347
7.54-11.160.72507
6.04-7.540.69606
5.18-6.040.67711
4.61-5.180.63789
4.19-4.610.55843
3.87-4.190.44912
3.61-3.870.36967
Phasing dmDelta phi final: 6.28 / Delta phi initial: 52.54 / FOM : 0.889 / Mask type: RMS / Method: FLIP / Reflection: 9114
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.24-502.0580.8791097
4.95-6.246.6970.9371037
4.33-4.955.9260.9611018
3.93-4.337.0160.936995
3.65-3.936.8330.919992
3.43-3.656.5820.9021002
3.26-3.436.40.882992
3.12-3.267.2280.822972
3-3.128.160.7631009

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0005refinement
SCALEPACKdata scaling
SOLVE2.03phasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.862 / SU B: 44.926 / SU ML: 0.376 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.283 861 9.8 %RANDOM
Rwork0.276 ---
obs0.277 8805 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.387 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2---2.36 Å20 Å2
3---4.72 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 52 12 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222205
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9852997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02823.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.40215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.432158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021657
X-RAY DIFFRACTIONr_nbd_refined0.2720.21173
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.26
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.21
X-RAY DIFFRACTIONr_mcbond_it1.0631.51355
X-RAY DIFFRACTIONr_mcangle_it1.93522122
X-RAY DIFFRACTIONr_scbond_it1.8983982
X-RAY DIFFRACTIONr_scangle_it2.8784.5875
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 60 -
Rwork0.371 556 -
all-616 -
obs--92.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35490.3511-0.94792.5406-0.87383.1287-0.0058-0.09320.03670.3729-0.0647-0.1490.13020.09970.0705-0.06230.0263-0.0276-0.0978-0.0114-0.047636.118917.40559.1371
21.85230.2458-2.40422.6999-0.40695.33290.4869-0.4814-0.0181-0.26-0.25830.3918-0.0267-0.6762-0.22860.0759-0.03980.10680.08390.0328-0.074720.309510.749318.7779
341.10781.53253.39582.46110.25060.2869-0.6678-1.58882.14191.0015-0.06820.74630.30330.39510.7359-0.06230.01080.05770.2801-0.0824-0.084227.204323.599411.6695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA507 - 7387 - 238
2X-RAY DIFFRACTION2AA748 - 779248 - 279
3X-RAY DIFFRACTION3AC900

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