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- PDB-6axj: Crystal structure of the Yaf9 YEATS domain bound to H3K27ac -

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Basic information

Entry
Database: PDB / ID: 6axj
TitleCrystal structure of the Yaf9 YEATS domain bound to H3K27ac
Components
  • ALY-SER-ALA-PRO-ALA
  • Protein AF-9 homolog
KeywordsTRANSCRIPTION / Epigenetic / Gene Regulation
Function / homology
Function and homology information


Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation ...Swr1 complex / NuA4 histone acetyltransferase complex / subtelomeric heterochromatin formation / Chromatin modifying enzymes / epigenetic regulation of gene expression / 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 / 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 / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm
Similarity search - Function
YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 ...YEATS domain / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein AF-9 homolog / Histone H3.1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.379 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Yaf9 subunit of the NuA4 and SWR1 complexes targets histone H3K27ac through its YEATS domain.
Authors: Klein, B.J. / Ahmad, S. / Vann, K.R. / Andrews, F.H. / Mayo, Z.A. / Bourriquen, G. / Bridgers, J.B. / Zhang, J. / Strahl, B.D. / Cote, J. / Kutateladze, T.G.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9 homolog
C: Protein AF-9 homolog
B: Protein AF-9 homolog
D: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
E: ALY-SER-ALA-PRO-ALA
H: ALY-SER-ALA-PRO-ALA
F: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,21322
Polymers81,9088
Non-polymers1,30514
Water12,268681
1
A: Protein AF-9 homolog
E: ALY-SER-ALA-PRO-ALA
hetero molecules

A: Protein AF-9 homolog
E: ALY-SER-ALA-PRO-ALA
hetero molecules

A: Protein AF-9 homolog
E: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,56018
Polymers61,4316
Non-polymers1,12912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8790 Å2
ΔGint-77 kcal/mol
Surface area23380 Å2
MethodPISA
2
C: Protein AF-9 homolog
F: ALY-SER-ALA-PRO-ALA
hetero molecules

C: Protein AF-9 homolog
F: ALY-SER-ALA-PRO-ALA
hetero molecules

C: Protein AF-9 homolog
F: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,28415
Polymers61,4316
Non-polymers8539
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7900 Å2
ΔGint-74 kcal/mol
Surface area22740 Å2
MethodPISA
3
B: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
hetero molecules

B: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
hetero molecules

B: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,53618
Polymers61,4316
Non-polymers1,10512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9920 Å2
ΔGint-73 kcal/mol
Surface area22400 Å2
MethodPISA
4
D: Protein AF-9 homolog
H: ALY-SER-ALA-PRO-ALA
hetero molecules

D: Protein AF-9 homolog
H: ALY-SER-ALA-PRO-ALA
hetero molecules

D: Protein AF-9 homolog
H: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,26015
Polymers61,4316
Non-polymers8299
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area8680 Å2
ΔGint-80 kcal/mol
Surface area22750 Å2
MethodPISA
5
A: Protein AF-9 homolog
B: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
E: ALY-SER-ALA-PRO-ALA
hetero molecules

A: Protein AF-9 homolog
B: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
E: ALY-SER-ALA-PRO-ALA
hetero molecules

A: Protein AF-9 homolog
B: Protein AF-9 homolog
G: ALY-SER-ALA-PRO-ALA
E: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,09636
Polymers122,86212
Non-polymers2,23424
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area21310 Å2
ΔGint-182 kcal/mol
Surface area43180 Å2
MethodPISA
6
C: Protein AF-9 homolog
D: Protein AF-9 homolog
H: ALY-SER-ALA-PRO-ALA
F: ALY-SER-ALA-PRO-ALA
hetero molecules

C: Protein AF-9 homolog
D: Protein AF-9 homolog
H: ALY-SER-ALA-PRO-ALA
F: ALY-SER-ALA-PRO-ALA
hetero molecules

C: Protein AF-9 homolog
D: Protein AF-9 homolog
H: ALY-SER-ALA-PRO-ALA
F: ALY-SER-ALA-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,54330
Polymers122,86212
Non-polymers1,68218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19180 Å2
ΔGint-186 kcal/mol
Surface area42890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.318, 140.318, 129.054
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Protein AF-9 homolog


Mass: 19361.684 Da / Num. of mol.: 4 / Fragment: UNP residues 8-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YAF9, YNL107W, N1966 / Production host: Escherichia coli (E. coli) / References: UniProt: P53930
#2: Protein/peptide
ALY-SER-ALA-PRO-ALA


Mass: 1115.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 277.14 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.0 M Ammonium Sulfate, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.379→35.1 Å / Num. obs: 37536 / % possible obs: 98.8 % / Redundancy: 3.6 % / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.379→35.079 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.54
RfactorNum. reflection% reflection
Rfree0.2269 2012 5.39 %
Rwork0.1787 --
obs0.1814 37345 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.379→35.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 0 80 681 5606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085090
X-RAY DIFFRACTIONf_angle_d0.9646882
X-RAY DIFFRACTIONf_dihedral_angle_d9.8643015
X-RAY DIFFRACTIONf_chiral_restr0.065719
X-RAY DIFFRACTIONf_plane_restr0.006875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.379-2.43850.31651410.24092471X-RAY DIFFRACTION97
2.4385-2.50440.32231470.24522553X-RAY DIFFRACTION99
2.5044-2.57810.31981400.22682525X-RAY DIFFRACTION99
2.5781-2.66120.3221450.22172510X-RAY DIFFRACTION99
2.6612-2.75630.26881440.212580X-RAY DIFFRACTION99
2.7563-2.86660.26831460.20932543X-RAY DIFFRACTION99
2.8666-2.9970.22161410.20242519X-RAY DIFFRACTION98
2.997-3.15490.26561470.19762518X-RAY DIFFRACTION98
3.1549-3.35250.22191420.17162549X-RAY DIFFRACTION98
3.3525-3.61110.22481450.16852503X-RAY DIFFRACTION98
3.6111-3.9740.1911450.1492537X-RAY DIFFRACTION98
3.974-4.5480.15711470.13822516X-RAY DIFFRACTION98
4.548-5.7260.19791400.14692514X-RAY DIFFRACTION98
5.726-35.08330.24211420.20492495X-RAY DIFFRACTION97
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)
10.8557-1.82240.32743.195-0.06271.2238-0.02150.1057-0.3965-0.61810.0501-0.14980.1187-0.0570.08740.3168-0.03330.01060.2968-0.04370.488765.216-30.688119.6274
25.1075-5.10014.68957.2318-1.8748.2882-0.4999-0.00130.86740.38170.74760.052-0.9566-0.97-0.29950.662-0.0028-0.04450.35710.15730.496158.45824.387714.5422
31.5984-1.07650.03466.46840.93732.93740.07490.0941-0.1505-0.1908-0.06130.068-0.1478-0.1071-0.00320.30090.0486-0.01920.30180.03250.289656.8826-17.320118.143
44.84534.02371.51034.87252.0161.3855-0.04520.0255-0.0645-0.6117-0.12380.58370.10170.08820.170.38380.068-0.06450.2971-0.02350.459361.2732-32.358316.5788
52.75766.1565-0.20037.77280.15261.54880.1057-0.30861.01330.0241-0.11910.4712-0.05860.03060.11470.32040.0250.02760.26930.01410.360664.14631.24229.5165
67.62272.45531.52443.99043.56143.18250.16591.2132-0.6529-0.1704-0.94271.11440.8868-0.99950.0830.6247-0.1186-0.04630.6681-0.07150.657237.13247.898324.2536
74.58463.1332-0.43623.4924-0.15492.8524-0.33230.1662-0.2107-0.4580.2408-0.09980.1975-0.07180.06040.3635-0.0325-0.00530.2424-0.02310.288356.350816.078526.5934
83.17593.3548-1.26023.4897-0.41852.03430.11390.03350.50060.0339-0.03820.2079-0.2277-0.0307-0.07560.3903-0.013-0.02720.29710.02260.274158.195723.786231.3763
95.67512.54510.9959.47750.61135.5578-0.67231.2934-0.0567-1.12540.4987-0.49210.54370.2975-0.110.4118-0.1930.09350.53770.02620.377477.067728.746122.1417
104.3799-4.56510.98845.8281-0.31371.62610.26310.2675-0.7074-0.1495-0.1960.13190.0624-0.0877-0.11260.3095-0.01960.00040.30230.01020.351364.1195-31.29341.2557
118.5563-6.0464-5.23475.41614.63324.09870.4173-0.7525-0.28370.1832-0.61850.4661-1.0204-0.8706-0.10170.66810.06920.07330.6239-0.0470.375137.1081-7.857246.4987
124.2621-2.88370.15884.5929-0.32972.2424-0.2655-0.15540.3180.43270.1527-0.2755-0.1341-0.01470.07890.37310.0355-0.01730.2431-0.02150.288658.7483-16.44244.1473
132.574-1.97811.01462.03460.77723.46670.48320.1553-0.87910.1308-0.31710.38440.2692-0.5797-0.26170.4971-0.05390.01640.3123-0.02750.412748.9084-21.935437.0027
146.4596-2.67273.20723.7123-0.62421.52560.32780.27540.08810.0648-0.04420.1840.06490.0154-0.1910.39480.0649-0.01690.27970.05860.28359.3582-28.997840.2226
158.7539-1.32651.45396.5493-0.84878.4296-0.6617-0.8484-0.11170.89280.1789-0.6708-0.58010.35020.33550.38370.1567-0.03350.38190.02950.415177.3256-28.650348.5138
160.25381.7182-0.17568.38890.07470.7033-0.058-0.09110.28680.09030.23220.0777-0.0903-0.0517-0.09020.32890.01770.02890.3558-0.04020.494765.126630.66351.143
172.96091.4023-3.24387.7323-3.89914.9276-0.64710.1406-1.1356-0.70440.68350.09281.7707-0.5709-0.48340.67910.06140.05480.39760.24820.605958.4307-4.470956.2631
181.24550.6993-0.65477.17950.69462.97210.1064-0.04790.21390.206-0.08020.12240.1564-0.14810.00920.2719-0.0518-0.0060.29450.03630.309556.950517.293552.6875
195.6342-3.5346-1.25445.19352.53662.3860.4136-0.04570.8138-0.7909-0.3896-0.7435-0.19070.3097-0.11260.3637-0.00790.060.36860.0040.448565.661225.400250.1285
207.71673.9506-3.79328.6579-0.02258.63860.1495-0.29050.65131.094-0.26370.46070.1064-0.2972-0.05270.5221-0.03340.12180.3531-0.05170.57757.05640.656958.5148
218.95494.43685.5433.3954.18675.1582-0.01320.41940.01210.02810.21641.42261.0909-1.06360.14510.4692-0.00660.03670.5670.00780.455939.2154-15.950832.8285
229.9508-7.1099-2.4275.2272.35289.80060.2578-1.39390.6544-0.09210.5262-0.3402-0.46661.3609-0.62280.6691-0.12510.01180.3903-0.05790.296264.2754-1.400728.2045
238.97535.93382.72476.02345.36676.89860.6910.74540.2230.11660.3233-0.96031.06111.6844-0.48360.55720.08530.05860.3760.02450.455764.35951.363442.7493
243.2636-1.6483-3.21152.73392.39793.52770.1597-0.80540.4652-0.02590.94460.8423-1.2895-0.9226-0.78890.57750.02310.00750.51390.01930.485339.198115.956438.0081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 40 )
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 168 )
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 26 )
6X-RAY DIFFRACTION6chain 'C' and (resid 27 through 40 )
7X-RAY DIFFRACTION7chain 'C' and (resid 41 through 100 )
8X-RAY DIFFRACTION8chain 'C' and (resid 101 through 156 )
9X-RAY DIFFRACTION9chain 'C' and (resid 157 through 169 )
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 26 )
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 40 )
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 108 )
13X-RAY DIFFRACTION13chain 'B' and (resid 109 through 144 )
14X-RAY DIFFRACTION14chain 'B' and (resid 145 through 156 )
15X-RAY DIFFRACTION15chain 'B' and (resid 157 through 169 )
16X-RAY DIFFRACTION16chain 'D' and (resid 6 through 26 )
17X-RAY DIFFRACTION17chain 'D' and (resid 27 through 40 )
18X-RAY DIFFRACTION18chain 'D' and (resid 41 through 144 )
19X-RAY DIFFRACTION19chain 'D' and (resid 145 through 156 )
20X-RAY DIFFRACTION20chain 'D' and (resid 157 through 169 )
21X-RAY DIFFRACTION21chain 'G' and (resid 28 through 31 )
22X-RAY DIFFRACTION22chain 'E' and (resid 28 through 31 )
23X-RAY DIFFRACTION23chain 'H' and (resid 28 through 31 )
24X-RAY DIFFRACTION24chain 'F' and (resid 28 through 31 )

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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