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- PDB-4lk9: Crystal Structure of MOZ double PHD finger histone H3 tail complex -

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Basic information

Entry
Database: PDB / ID: 4lk9
TitleCrystal Structure of MOZ double PHD finger histone H3 tail complex
Components
  • Histone H3.1
  • Histone acetyltransferase KAT6A
KeywordsTRANSFERASE / zinc finger / plant homeodomain finger / double PHD finger / DPF / histone acetyltransferase / histone H3 / H3 tail
Function / homology
Function and homology information


histone H3 acetyltransferase activity / myeloid cell differentiation / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / protein acetylation / histone acetyltransferase activity / acetyltransferase activity / chromosome organization / Chromatin modifying enzymes ...histone H3 acetyltransferase activity / myeloid cell differentiation / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / protein acetylation / histone acetyltransferase activity / acetyltransferase activity / chromosome organization / Chromatin modifying enzymes / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / 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 / transcription coregulator activity / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / PML body / B-WICH complex positively regulates rRNA expression / 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 / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / cellular senescence / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / nuclear speck / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / 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 / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.6 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.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.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

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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)18,0236
Polymers17,7612
Non-polymers2624
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-3 kcal/mol
Surface area8580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.519, 70.519, 96.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological assembly is the same as asymmetric unit

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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: 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: 2261.650 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.: 160 / 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: 3.39 Å3/Da / Density % sol: 63.7 %
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: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.57→57.003 Å / Num. all: 32766 / Num. obs: 32766 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.064 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.6950.74612346746940.74699.7
1.69-1.7950.481.62227044520.4899.7
1.79-1.9150.292.72099941920.2999.7
1.91-2.0750.1684.61963839270.16899.9
2.07-2.2650.0987.81806236320.09899.9
2.26-2.5350.07110.61641333110.071100
2.53-2.924.90.05313.51447029420.05399.8
2.92-3.584.90.03817.41218424950.03899.3
3.58-5.064.80.02821.8941019700.02899.4
5.06-49.8644.40.03319.1507811510.03398

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→49.864 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8887 / SU ML: 0.14 / σ(F): 0 / Phase error: 17.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1863 1592 5.09 %
Rwork0.1635 --
obs0.1647 31295 95.08 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.97 Å2 / Biso mean: 27.2472 Å2 / Biso min: 10.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 4 160 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191114
X-RAY DIFFRACTIONf_angle_d1.6481477
X-RAY DIFFRACTIONf_chiral_restr0.116158
X-RAY DIFFRACTIONf_plane_restr0.008195
X-RAY DIFFRACTIONf_dihedral_angle_d14.76437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.65170.27151250.25252361248685
1.6517-1.71070.25011400.21992498263889
1.7107-1.77920.18511320.20582548268092
1.7792-1.86020.21971480.18332585273393
1.8602-1.95820.18651410.16972697283896
1.9582-2.08090.17981480.16282723287197
2.0809-2.24160.15681430.15492766290998
2.2416-2.46720.17631560.15822806296299
2.4672-2.82420.18631440.16452855299999
2.8242-3.5580.18531580.16252863302199
3.558-49.88870.17911570.14443001315898
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)
13.48730.41760.48520.6083-0.06820.3562-0.49370.14850.43760.0709-0.0068-0.2273-0.4920.3550.27030.1966-0.1166-0.10310.29110.11220.256715.879646.372730.8713
24.0439-1.10610.87032.9618-0.7663.6975-0.16240.18010.0684-0.0167-0.03030.01560.0716-0.01480.14170.1217-0.0616-0.03060.06830.04620.10939.923740.611932.0548
33.2248-1.7269-1.17383.1976-0.87533.41340.1695-0.0299-0.36570.0408-0.15210.00040.44360.0416-0.02570.2203-0.0073-0.04810.13810.05130.176719.369728.072939.6344
43.4292-0.2955-2.93253.14381.10426.15760.19290.3705-0.6132-0.6094-0.06920.6740.6018-0.39130.00030.2745-0.0837-0.06830.18640.04020.28296.978530.195129.5819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 190:214 )A190 - 214
2X-RAY DIFFRACTION2( CHAIN A AND RESID 215:280 )A215 - 280
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 281:315 OR RESID 401:401 ) )A281 - 315
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 281:315 OR RESID 401:401 ) )A401
5X-RAY DIFFRACTION4( CHAIN B AND RESID 1:13 )B1 - 13

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