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- PDB-4lka: Crystal Structure of MOZ double PHD finger histone H3K9ac complex -

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Basic information

Entry
Database: PDB / ID: 4lka
TitleCrystal Structure of MOZ double PHD finger histone H3K9ac complex
Components
  • Histone H3.1
  • Histone acetyltransferase KAT6A
KeywordsTRANSFERASE / zinc finger / plant homeodomain finger / double PHD finger / DPF / histone acetyltransferase / histone H3 tail acetylated at K9
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 / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis ...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 / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / protein acetylation / acetyltransferase activity / chromosome organization / Chromatin modifying enzymes / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of signal transduction by p53 class mediator / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription coregulator activity / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / PML body / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / cellular senescence / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription factor binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / transcription coactivator activity / nuclear speck / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / 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 ...: / 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 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / PHD-finger / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsDreveny, I. / Deeves, S.E. / Yue, B. / Heery, D.M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The double PHD finger domain of MOZ/MYST3 induces alpha-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification.
Authors: Dreveny, I. / Deeves, S.E. / Fulton, J. / Yue, B. / Messmer, M. / Bhattacharya, A. / Collins, H.M. / Heery, D.M.
History
DepositionJul 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT6A
B: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0646
Polymers17,8022
Non-polymers2624
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.455, 70.455, 96.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Histone acetyltransferase KAT6A / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt- ...MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 3 / MYST-3 / Monocytic leukemia zinc finger protein / Runt-related transcription factor-binding protein 2 / Zinc finger protein 220


Mass: 15499.267 Da / Num. of mol.: 1 / Fragment: unp residues 194-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3FA, HIST1H3A, KAT6A, MOZ, MYST3, RUNXBP2, ZNF220 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q92794, histone acetyltransferase
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j Histone H3/k / Histone H3/l


Mass: 2302.679 Da / Num. of mol.: 1 / Fragment: unp residues 2-22 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: P68431
#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.: 152 / 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: 3.36 Å3/Da / Density % sol: 63.38 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM Na-Hepes, 1.4 M sodium citrate, pH 7.5, vapor diffusion, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 1.61→48.19 Å / Num. obs: 32149 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Rmerge(I) obs: 0.076

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4LK9

4lk9


Resolution: 1.61→44.255 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8795 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 1607 5.01 %
Rwork0.1641 --
obs0.1652 32092 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.91 Å2 / Biso mean: 31.7495 Å2 / Biso min: 13.94 Å2
Refinement stepCycle: LAST / Resolution: 1.61→44.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 4 152 1217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091148
X-RAY DIFFRACTIONf_angle_d1.171533
X-RAY DIFFRACTIONf_chiral_restr0.08165
X-RAY DIFFRACTIONf_plane_restr0.006205
X-RAY DIFFRACTIONf_dihedral_angle_d14.908454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.61-1.6620.29021180.221227392857
1.662-1.72140.22331380.192127182856
1.7214-1.79030.20681410.184327162857
1.7903-1.87180.22431410.173427402881
1.8718-1.97050.20231390.171627392878
1.9705-2.09390.18761400.161627502890
2.0939-2.25560.18311460.158327492895
2.2556-2.48260.19451730.161227422915
2.4826-2.84170.21511450.169527952940
2.8417-3.58010.17761550.167228212976
3.5801-44.27210.15931710.151729763147
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)
11.8703-0.28550.39271.463-0.52961.12-0.37260.18350.615-0.0387-0.1159-0.3916-0.35850.55640.4050.2534-0.1161-0.0750.35180.12840.3249-16.107411.7103-16.5072
23.2513-0.06310.17332.51370.47373.8939-0.2675-0.22160.23720.1367-0.05620.403-0.2688-0.57780.26290.21070.027-0.05740.2135-0.00960.2515-36.010412.9567-16.5564
33.1812-0.96940.66662.3315-1.24393.5729-0.10620.22330.0327-0.0702-0.0743-0.14070.11320.18080.15510.1642-0.0441-0.02410.13510.04590.1748-21.83124.3591-16.4385
43.2723-0.9905-0.29822.8002-0.57982.3460.1863-0.0276-0.45920.0086-0.1062-0.03660.59190.0665-0.07140.30870.005-0.03870.18360.04570.2343-16.7274-7.5731-10.106
54.16270.0262-0.98561.9477-1.83874.59950.0926-0.0142-0.4326-0.2907-0.0220.19510.7987-0.2027-0.09880.3139-0.062-0.04030.18040.0320.2866-25.6919-6.348-16.9826
65.0825-0.202-2.44837.62782.30246.59760.22840.7199-0.9855-0.5726-0.09711.16671.0383-0.4223-0.00590.4304-0.085-0.13920.3475-0.02450.417-31.5761-4.1099-20.6336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 190 through 209 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 229 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 230 through 274 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 315)A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 7 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 12)B0

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