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- PDB-7f4a: Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide -

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Basic information

Entry
Database: PDB / ID: 7f4a
TitleCrystal structure of Taf14 YEATS domain in complex with H3K9bz peptide
Components
  • Histone H3
  • Transcription initiation factor TFIID subunit 14
KeywordsNUCLEAR PROTEIN / Histone modification / Histone benzoylation / YEATS domain / protein-protein interaction
Function / homology
Function and homology information


NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / transcription factor TFIIF complex / mediator complex / Ino80 complex / Oxidative Stress Induced Senescence / SWI/SNF complex / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / intracellular copper ion homeostasis / RNA polymerase II preinitiation complex assembly / CENP-A containing nucleosome / aerobic respiration / transcription initiation at RNA polymerase II promoter / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / transcription by RNA polymerase II / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. ...SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile. / NET domain / Bromodomain extra-terminal - transcription regulation / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Transcription initiation factor TFIID subunit 14 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, D. / Yan, F. / Yong, C.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37010303 China
National Natural Science Foundation of China (NSFC)31970576 China
CitationJournal: Nat Commun / Year: 2022
Title: Global profiling of regulatory elements in the histone benzoylation pathway.
Authors: Wang, D. / Yan, F. / Wu, P. / Ge, K. / Li, M. / Li, T. / Gao, Y. / Peng, C. / Chen, Y.
History
DepositionJun 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 14
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)16,6742
Polymers16,6742
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-1 kcal/mol
Surface area7720 Å2
Unit cell
Length a, b, c (Å)113.786, 113.786, 26.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcription initiation factor TFIID subunit 14 / Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling ...Actin non-complementing mutant 1 / Chromosome stability protein 10 / SWI/SNF chromatin-remodeling complex subunit TAF14 / SWI/SNF complex 29 kDa subunit / SWI/SNF complex subunit TAF14 / TBP-associated factor 14 / TBP-associated factor 30 kDa / Transcription factor G 30 kDa subunit / Transcription initiation factor TFIIF 30 kDa subunit


Mass: 15637.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W / Production host: Escherichia coli (E. coli) / References: UniProt: P35189
#2: Protein/peptide Histone H3


Mass: 1036.121 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P61830
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 48% PEG 600, 0.04M citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 13600 / % possible obs: 98.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.033 / Rrim(I) all: 0.1 / Χ2: 0.981 / Net I/σ(I): 4.9 / Num. measured all: 125173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.037.20.7335970.7940.2780.7870.98187.5
2.03-2.077.20.6616410.8240.2520.710.99194
2.07-2.117.40.6286440.8350.2380.6731.01696.4
2.11-2.1580.5756520.8790.210.6131.01896.9
2.15-2.28.70.546940.8880.190.5740.97198.9
2.2-2.259.30.5136600.9380.1750.5430.99799.8
2.25-2.319.80.4496680.9370.1510.4740.975100
2.31-2.379.90.3857060.9560.1280.4061.014100
2.37-2.449.80.3326800.9650.1110.351.019100
2.44-2.529.30.2656690.9740.0910.2811.022100
2.52-2.619.30.2346900.9720.0810.2481.012100
2.61-2.7110.10.2136820.980.0710.2251.005100
2.71-2.8410.20.1616910.9890.0530.171.045100
2.84-2.99100.1416930.9910.0470.1491.065100
2.99-3.179.80.1046730.9960.0350.111.031100
3.17-3.429.20.0836990.9960.0290.0881.027100
3.42-3.7610.20.0657050.9980.0220.0690.978100
3.76-4.31100.0556940.9980.0180.0580.906100
4.31-5.439.10.0477130.9990.0170.0490.837100
5.43-509.10.0457490.9970.0160.0480.73599.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D7E

5d7e


Resolution: 2→24.111 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 634 4.93 %
Rwork0.176 12225 -
obs0.1774 12859 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.9 Å2 / Biso mean: 34.8057 Å2 / Biso min: 12.78 Å2
Refinement stepCycle: final / Resolution: 2→24.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 110 1267
Biso mean---42.17 -
Num. residues----142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.1540.24331020.2254183772
2.154-2.37060.25961360.2113247195
2.3706-2.71330.21991460.19182569100
2.7133-3.41690.22741090.17792641100
3.4169-24.1110.16751410.15262707100
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)
12.07311.81261.32818.65653.29981.85030.01880.0478-0.07830.1472-0.0224-0.4582-0.20770.2658-0.03480.1413-0.0351-0.00180.19250.0360.1772-39.53419.8560.4136
25.0491-1.3544-3.24784.22761.475.87550.1941-0.28121.044-0.20110.5453-0.0584-0.2234-0.7386-0.71670.3277-0.0858-0.05140.27660.01360.6742-39.897338.27773.7199
30.63691.85790.76127.73592.75941.3944-0.27390.280.2025-0.4492-0.29090.2258-0.38470.4139-0.2070.3446-0.1966-0.06910.16040.10150.3146-41.19819.6333-1.9926
47.71421.98141.06024.6333-3.48317.2296-0.06051.2229-0.818-0.5768-0.0508-1.00120.07270.91760.08120.2551-0.05250.11540.347-0.06940.3258-38.16942.8889-7.264
52.27181.36890.87998.9863.5665.34070.4972-0.20111.12090.8511-0.72891.4104-0.2093-0.56220.28790.3137-0.05450.13450.1545-0.06070.5335-51.644518.47013.5501
64.44560.4342-0.4666.03590.03246.5706-0.03320.34691.032-0.49540.11661.2101-0.19280.1683-0.02060.3118-0.094-0.12390.16580.14320.4446-50.232515.7959-4.5016
77.25790.39941.5563.5059-2.89922.8842-0.1887-0.14391.13640.3366-0.24120.9201-0.6156-0.21570.33830.4164-0.1031-0.08010.19240.05150.5306-44.614927.96562.0485
84.70664.82311.98557.06282.44144.48770.3209-0.52110.5981-0.0672-0.53510.5644-0.3175-0.03370.15920.1797-0.04680.0520.1299-0.01520.2233-50.37349.66143.5956
96.09687.17092.09978.73911.96561.32120.6661-0.60660.19851.1864-0.80870.0832-0.0530.02950.10640.3413-0.09390.00440.25270.05230.2022-46.250210.57316.8621
106.0916-0.5408-2.05027.7336.14012.00870.040.38580.45070.00730.0874-0.6998-0.45581.76360.00460.34-0.1714-0.07160.46610.16040.3855-33.141424.44584.1169
118.65775.54552.16554.03281.74390.90010.18140.3199-0.48910.57860.0789-0.89640.01220.2695-0.13830.2314-0.0374-0.04950.20730.03630.2188-39.00157.29893.2145
124.03973.2358-0.27037.2396-1.24233.68470.49460.7566-0.8301-0.1537-0.0993-0.49550.0837-0.0791-0.33530.27360.0516-0.01530.1939-0.03310.1873-47.9276-5.8002-5.3026
130.6211-0.96821.01319.43253.62178.62040.4197-0.21570.35090.3423-0.0933-0.1776-0.05521.351-0.4840.645-0.3439-0.12250.545-0.00910.3847-34.82527.967110.5528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )A2 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 29 )A18 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 38 )A30 - 38
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 50 )A39 - 50
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 65 )A51 - 65
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 75 )A66 - 75
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 83 )A76 - 83
8X-RAY DIFFRACTION8chain 'A' and (resid 84 through 95 )A84 - 95
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 105 )A96 - 105
10X-RAY DIFFRACTION10chain 'A' and (resid 106 through 110 )A106 - 110
11X-RAY DIFFRACTION11chain 'A' and (resid 111 through 121 )A111 - 121
12X-RAY DIFFRACTION12chain 'A' and (resid 122 through 137 )A122 - 137
13X-RAY DIFFRACTION13chain 'B' and (resid 5 through 8 )B5 - 8

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