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- PDB-5u2j: MORF double PHD finger (DPF) in complex with histone H3K14bu -

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Basic information

Entry
Database: PDB / ID: 5u2j
TitleMORF double PHD finger (DPF) in complex with histone H3K14bu
Components
  • Histone H3K14bu
  • Histone acetyltransferase KAT6B
KeywordsHYDROLASE / transcription / epigenetics / acyllysine
Function / homology
Function and homology information


histone H3K14 acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / Chromatin modifying enzymes / epigenetic regulation of gene expression / histone acetyltransferase activity / histone acetyltransferase / telomere organization ...histone H3K14 acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / Chromatin modifying enzymes / epigenetic regulation of gene expression / histone acetyltransferase activity / histone acetyltransferase / 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 / 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 / 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 / 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 / Estrogen-dependent gene expression / transcription coactivator activity / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / protein-containing complex binding / 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 / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
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
Histone H3.1 / Histone acetyltransferase KAT6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAndrews, F.H. / Klein, B.J. / Kutateladze, T.G.
CitationJournal: Structure / Year: 2017
Title: Recognition of Histone H3K14 Acylation by MORF.
Authors: Klein, B.J. / Simithy, J. / Wang, X. / Ahn, J. / Andrews, F.H. / Zhang, Y. / Cote, J. / Shi, X. / Garcia, B.A. / Kutateladze, T.G.
History
DepositionNov 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Histone H3K14bu
A: Histone acetyltransferase KAT6B
B: Histone acetyltransferase KAT6B
C: Histone H3K14bu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,93712
Polymers28,4134
Non-polymers5238
Water4,792266
1
D: Histone H3K14bu
B: Histone acetyltransferase KAT6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4686
Polymers14,2072
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area7580 Å2
MethodPISA
2
A: Histone acetyltransferase KAT6B
C: Histone H3K14bu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4686
Polymers14,2072
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-4 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.540, 69.190, 69.930
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Histone H3K14bu


Mass: 1731.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#2: Protein Histone acetyltransferase KAT6B / Histone acetyltransferase MOZ2 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 4 / MYST-4 / Monocytic ...Histone acetyltransferase MOZ2 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 4 / MYST-4 / Monocytic leukemia zinc finger protein-related factor


Mass: 12474.659 Da / Num. of mol.: 2 / Fragment: UNP residues 211-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6B, KIAA0383, MORF, MOZ2, MYST4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8WYB5, histone acetyltransferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.1 M sodium citrate tribasic, 0.1 M sodium hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: AREA DETECTOR / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→34.7 Å / Num. obs: 40091 / % possible obs: 99.9 % / Redundancy: 9.5 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.693 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 2019 5.04 %
Rwork0.1907 --
obs0.1931 40091 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 8 266 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061984
X-RAY DIFFRACTIONf_angle_d0.9042661
X-RAY DIFFRACTIONf_dihedral_angle_d18.1581253
X-RAY DIFFRACTIONf_chiral_restr0.049282
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.39591170.35792478X-RAY DIFFRACTION89
1.64-1.68440.34781560.33332569X-RAY DIFFRACTION94
1.6844-1.73390.35341320.2992745X-RAY DIFFRACTION99
1.7339-1.78990.27691300.26372759X-RAY DIFFRACTION100
1.7899-1.85390.26311230.23712712X-RAY DIFFRACTION100
1.8539-1.92810.26211410.23212765X-RAY DIFFRACTION100
1.9281-2.01580.21581450.20612751X-RAY DIFFRACTION100
2.0158-2.12210.20781410.19112750X-RAY DIFFRACTION100
2.1221-2.2550.20151380.17692756X-RAY DIFFRACTION100
2.255-2.42910.2541520.19332727X-RAY DIFFRACTION100
2.4291-2.67350.2511480.18342767X-RAY DIFFRACTION100
2.6735-3.06010.22721930.18042734X-RAY DIFFRACTION100
3.0601-3.85470.2081390.16122766X-RAY DIFFRACTION100
3.8547-34.70070.23031640.15052793X-RAY DIFFRACTION99
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)
13.3359-3.4585-0.07945.87543.31595.26820.0450.4974-0.616-0.1433-0.20010.85070.0152-0.17780.14140.2312-0.0489-0.06810.2946-0.02220.330755.6482-18.1031-2.6101
26.03240.20814.75821.3730.34884.21340.00550.78380.2221-0.57810.10140.0448-0.05370.35930.01990.2993-0.02940.02490.2317-0.05160.188878.47165.545232.0131
35.5468-3.36184.78784.4484-0.0828.86620.2551-0.1126-0.18170.23880.11720.03280.4874-0.0715-0.33450.2322-0.0345-0.01410.1795-0.04430.26782.62264.297143.0169
49.79234.17926.33915.64393.19374.5181-0.099-0.2233-0.12420.30360.2784-0.3230.130.2375-0.09720.21110.0424-0.01250.197-0.03080.21884.773-0.134437.7438
53.35550.43470.32187.72061.54054.2197-0.0220.0328-0.05390.21630.1275-0.24320.06140.3333-0.09360.1033-0.0059-0.0080.1604-0.03330.166679.6422-5.710133.4377
64.58721.7113.86612.84291.3635.0389-0.1496-0.36450.4443-0.0334-0.13130.3821-0.2832-0.46340.22630.20410.02880.00080.2246-0.02570.212568.4626-7.392723.6604
73.05161.17672.28815.2416-0.83342.9584-0.0364-0.1532-0.16980.09840.20070.1564-0.0174-0.2569-0.13860.18380.00820.00050.20460.03370.1667.3927-18.031326.9624
87.91673.1798-4.50689.1713-2.32422.8523-0.2609-0.1023-0.0576-0.20610.1989-0.39470.31670.22180.07540.16640.0237-0.01240.16180.03020.141574.934-21.834527.5634
95.4548-3.4482.6618.2798-4.90223.2861-0.1133-0.434-0.07380.23380.1689-0.0233-0.1978-0.2756-0.0370.2207-0.0056-0.04990.2222-0.04920.223966.3284-28.83840.9354
108.4205-1.01471.47533.118-4.16536.74870.24830.51840.0605-0.8157-0.1223-0.5165-0.12140.5613-0.10510.2995-0.00580.01730.2225-0.07290.334872.7257-26.6378-8.0576
116.82831.9041.8781.9149-1.08112.89290.0689-0.2766-0.24930.06860.0437-0.4466-0.08390.9502-0.21420.1923-0.0089-0.00620.2175-0.07960.260672.9533-22.8427-0.2878
123.1629-0.7678-1.9553.24972.33145.4996-0.04260.0390.0396-0.0827-0.1392-0.0692-0.37430.15930.08520.1871-0.0233-0.04520.1432-0.03150.174565.7482-20.71121.4079
133.80220.1798-2.36754.90774.13735.34730.2785-0.08240.0293-0.89440.2757-0.4863-0.46810.7634-0.57050.2821-0.05370.0120.2657-0.03280.317471.5813-11.3363.0474
141.7074-0.604-1.12331.3623-0.03631.57140.1148-0.0120.0076-0.09160.01410.47920.0542-0.3496-0.0820.1712-0.00670.00580.2510.02650.227157.2496-16.039911.617
158.48181.12861.59433.97720.93645.86180.1993-0.2272-0.2102-0.1519-0.14570.4608-0.0407-0.5387-0.04720.14970.002-0.03270.19210.02260.197457.9009-9.94065.5517
161.8634-0.9611.34162.38140.85272.5311-0.0560.1602-0.17520.2411-0.13030.42080.1074-0.35770.25870.15140.0340.00710.24110.04790.310652.4755-6.987911.1377
175.4912-0.8706-3.97265.84810.71392.87060.14860.27660.3271-0.48570.03840.9586-0.755-0.9685-0.22790.25140.0614-0.00380.30960.06430.400651.1069-0.64655.772
186.9967-1.92945.13458.4263-1.17483.974-0.37880.05210.4220.32920.14990.0407-0.5402-0.09940.16340.20910.0052-0.01320.20380.03930.183762.3163-1.20667.3388
192.0522.79280.8985.80452.46611.3202-0.0515-0.29670.8133-0.1063-0.17642.4552-0.2342-0.25810.32850.2677-0.00420.05370.3122-0.05410.539167.1488-5.032936.5906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 222 )
4X-RAY DIFFRACTION4chain 'A' and (resid 223 through 229 )
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 302 )
8X-RAY DIFFRACTION8chain 'A' and (resid 303 through 312 )
9X-RAY DIFFRACTION9chain 'B' and (resid 204 through 213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 223 )
11X-RAY DIFFRACTION11chain 'B' and (resid 224 through 229 )
12X-RAY DIFFRACTION12chain 'B' and (resid 230 through 245 )
13X-RAY DIFFRACTION13chain 'B' and (resid 246 through 254 )
14X-RAY DIFFRACTION14chain 'B' and (resid 255 through 274 )
15X-RAY DIFFRACTION15chain 'B' and (resid 275 through 286 )
16X-RAY DIFFRACTION16chain 'B' and (resid 287 through 292 )
17X-RAY DIFFRACTION17chain 'B' and (resid 293 through 302 )
18X-RAY DIFFRACTION18chain 'B' and (resid 303 through 312 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 16 )

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