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- PDB-3v43: Crystal structure of MOZ -

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Basic information

Entry
Database: PDB / ID: 3v43
TitleCrystal structure of MOZ
Components
  • Histone H3.1Histone H3
  • Histone acetyltransferase KAT6A
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / MOZ / PHD finger / Histone H3 / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation ...histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation / acetyltransferase activity / chromosome organization / Chromatin modifying enzymes / epigenetic regulation of gene expression / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / regulation of signal transduction by p53 class mediator / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / transcription coregulator activity / 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 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PML body / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / cellular senescence / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / 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 / positive regulation of gene expression / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / 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 / 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 / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Histone H3.1 / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsQiu, Y. / Li, F.
CitationJournal: Genes Dev. / Year: 2012
Title: Combinatorial readout of unmodified H3R2 and acetylated H3K14 by the tandem PHD finger of MOZ reveals a regulatory mechanism for HOXA9 transcription
Authors: Qiu, Y. / Liu, L. / Zhao, C. / Han, C. / Li, F. / Zhang, J. / Wang, Y. / Li, G. / Mei, Y. / Wu, M. / Wu, J. / Shi, Y.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Mar 20, 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_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 KAT6A
Q: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0917
Polymers14,7702
Non-polymers3215
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.080, 57.630, 76.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 12779.969 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 204-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6A, MOZ, MYST3, RUNXBP2, ZNF220 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92794, histone acetyltransferase
#2: Protein/peptide Histone H3.1 / Histone H3 / 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: 1990.315 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-19 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / 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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.62 Å3/Da / Density % sol: 53.02 % / Mosaicity: 0.46 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 0.1M tri-sodium citrate, 30% w/v PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 13.6 % / Av σ(I) over netI: 7.6 / Rsym value: 0.063 / D res high: 1.467 Å / D res low: 38.255 Å / Num. obs: 27192 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
1.471.5597.810.4560.45612.9
1.551.6410010.2820.28214
1.641.7510010.1760.17614
1.751.8910010.1160.11614
1.892.0710010.0890.08913.9
2.072.3210010.0590.05913.8
2.322.6899.910.0510.05113.6
2.683.2899.610.0580.05813.3
3.284.6499.610.0390.03912.4
4.6438.2698.110.0350.03512.3
ReflectionResolution: 1.467→38.255 Å / Num. all: 27192 / Num. obs: 27192 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rsym value: 0.063 / Net I/σ(I): 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.47-1.5512.90.4930.4561.64920738200.1350.4930.4565.897.8
1.55-1.64140.3060.2822.65199837020.0810.3060.2829.5100
1.64-1.75140.1930.1764.14925835220.0510.1930.17614.1100
1.75-1.89140.1320.11664539732430.0350.1320.11619.6100
1.89-2.0713.90.1040.0896.94224630420.0280.1040.08926.3100
2.07-2.3213.80.0720.059113806727560.0190.0720.05933.6100
2.32-2.6813.60.0660.051123312124280.0180.0660.05137.199.9
2.68-3.2813.30.070.0589.82746020720.0190.070.05843.399.6
3.28-4.6412.40.0490.03915.82036116440.0140.0490.0395099.6
4.64-38.25512.30.0510.03517.8118039630.0140.0510.03547.898.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
SHELXphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→19.13 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.658 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 1354 5.1 %RANDOM
Rwork0.1529 ---
obs0.1541 26750 98.44 %-
all-27138 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 127.42 Å2 / Biso mean: 20.4177 Å2 / Biso min: 8.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.47→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 8 157 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022942
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9741272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90222.82139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24215168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5691510
X-RAY DIFFRACTIONr_chiral_restr0.0910.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022718
X-RAY DIFFRACTIONr_mcbond_it1.2121.5609
X-RAY DIFFRACTIONr_mcangle_it2.0382982
X-RAY DIFFRACTIONr_scbond_it2.8923333
X-RAY DIFFRACTIONr_scangle_it4.3964.5287
X-RAY DIFFRACTIONr_rigid_bond_restr1.2133942
LS refinement shellResolution: 1.467→1.505 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 87 -
Rwork0.206 1683 -
all-1770 -
obs--93.9 %

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