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- PDB-6lsb: Crystal Structure of DPF domain of MOZ in complex with H3K14bz peptide -

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Basic information

Entry
Database: PDB / ID: 6lsb
TitleCrystal Structure of DPF domain of MOZ in complex with H3K14bz peptide
Components
  • Histone H3
  • Histone acetyltransferase KAT6A
KeywordsTRANSCRIPTION / DPF domain / histone Kbz modification
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 / cellular senescence / nucleosome / nucleosome assembly / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / protein heterodimerization activity / 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
: / 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. ...: / 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 / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, H.T. / Ren, X.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725014, 31871283, 31922016 China
National Basic Research Program of China (973 Program)2016YFA0500700 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins.
Authors: Ren, X. / Zhou, Y. / Xue, Z. / Hao, N. / Li, Y. / Guo, X. / Wang, D. / Shi, X. / Li, H.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Source and taxonomy
Category: pdbx_entity_src_syn / struct_ref ...pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT6A
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9276
Polymers17,6662
Non-polymers2624
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.187, 48.187, 116.848
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone acetyltransferase KAT6A / MOZ


Mass: 14930.603 Da / Num. of mol.: 1 / Fragment: DPF domain of MOZ
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOZ / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92794, histone acetyltransferase
#2: Protein/peptide Histone H3


Mass: 2735.196 Da / Num. of mol.: 1 / Fragment: histone H3 peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P22843*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.4 M sodium citrate tribasic dehydrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10923 / % possible obs: 97.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.043 / Rrim(I) all: 0.101 / Χ2: 2.623 / Net I/σ(I): 10.9 / Num. measured all: 53278
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.035.50.4125280.9110.1690.4471.27898.7
2.03-2.075.40.3875320.9230.1620.4221.47699.1
2.07-2.115.40.3575480.9460.150.3891.43799.8
2.11-2.155.40.2955390.9680.1250.3221.7999.8
2.15-2.25.30.2875490.9520.1240.3151.78999.1
2.2-2.255.30.2635470.9660.1130.2872.17100
2.25-2.3150.235490.9790.1040.2542.25499.6
2.31-2.3750.2225420.9720.1010.2462.221100
2.37-2.444.80.2015470.9840.0930.2232.52898.7
2.44-2.524.30.1825570.970.0930.2052.71799.8
2.52-2.6150.1575440.9880.0720.1732.87198.6
2.61-2.7150.1435450.9850.0660.1582.98499.8
2.71-2.844.80.1245410.9880.0590.1383.497.8
2.84-2.994.70.1125580.9920.0540.1253.36498.2
2.99-3.174.60.0965380.990.0480.1083.53797.8
3.17-3.424.30.0795430.9940.0410.093.7695.4
3.42-3.763.80.0695180.9940.0380.0794.17191.4
3.76-4.314.50.0655200.9930.0310.0724.08290.1
4.31-5.434.70.0535610.9970.0250.0593.30494.9
5.43-504.50.0486170.9970.0240.0542.98895.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B76

5b76


Resolution: 2→39.3 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1055 9.69 %
Rwork0.158 9827 -
obs0.1626 10882 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.83 Å2 / Biso mean: 39.2595 Å2 / Biso min: 19.02 Å2
Refinement stepCycle: final / Resolution: 2→39.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 4 89 1229
Biso mean--28.77 41.45 -
Num. residues----147
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.090.25611420.19051209135199
2.09-2.20.22541370.16381204134199
2.2-2.340.21671260.16112281354100
2.34-2.520.23851570.16721223138099
2.52-2.780.22281190.15951233135299
2.78-3.180.19331280.17181240136898
3.18-40.18661060.14991210131692
4.01-39.30.1911400.14831280142095
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)
12.94120.3436-1.08740.39190.12331.5708-0.41770.00030.0757-0.06120.21180.13690.0724-0.10190.19490.3543-0.05310.03820.1669-0.02280.26233.9183-24.22925.7449
23.76740.19351.35362.7472-0.85392.3451-0.46030.5044-0.1936-0.03260.12150.1776-0.00310.32580.27610.4247-0.13170.09670.2141-0.04230.267621.6226-18.4016-1.5708
36.4449-1.6603-2.04053.1962-0.15572.3332-0.4126-0.2012-0.8692-0.23510.1545-0.47970.02170.2860.21260.3188-0.03620.04150.2641-0.02840.306423.491-20.81152.7681
42.49330.4632-0.04390.16040.26361.18-0.10290.0509-0.1452-0.05710.07890.1383-0.04070.05220.06330.2805-0.037-0.01260.16920.02330.228711.93-18.8839.2004
54.38480.5778-0.93562.62660.14843.79480.0372-0.27690.69830.20790.05670.1124-0.38850.1089-0.05310.31890.00550.0170.1911-0.02170.30664.7108-12.823221.4412
61.73440.5123-1.84711.5899-0.62262.48150.57820.00790.5203-0.6025-0.1765-0.1115-0.8288-0.0119-0.31130.5927-0.04510.03660.26250.01120.417213.1306-6.837913.2326
72.98290.39750.29832.41920.26665.66480.00510.588-0.1286-0.76250.41340.4499-0.0328-0.8055-0.27160.5889-0.16-0.15980.46020.08890.443615.1052-11.4855-6.7266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 193 through 209 )A193 - 209
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 219 )A210 - 219
3X-RAY DIFFRACTION3chain 'A' and (resid 220 through 229 )A220 - 229
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 264 )A230 - 264
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 313 )A265 - 313
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 11 )B1 - 11
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 26 )B12 - 26

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