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- PDB-7f5m: Crystal structure of Sas5 YEATS domain in complex with H3K27bz peptide -

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Basic information

Entry
Database: PDB / ID: 7f5m
TitleCrystal structure of Sas5 YEATS domain in complex with H3K27bz peptide
Components
  • LYS-GLN-LEU-ALA-SER-LYS-ALA-ALA-ARG-LBZ-SER-ALA-PRO-SER-THR-GLY-GLY-VAL-LYS-TYR
  • Something about silencing protein 5
KeywordsNUCLEAR PROTEIN / histone modification / histone benzoylation / protein-protein interaction / YEATS domain
Function / homology
Function and homology information


SAS acetyltransferase complex / RNA Polymerase II Transcription Elongation / : / RNA Polymerase II Pre-transcription Events / acetyltransferase activity / subtelomeric heterochromatin formation / histone acetyltransferase activity / chromosome, telomeric region / regulation of DNA-templated transcription / chromatin
Similarity search - Function
SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / YEATS / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
Something about silencing protein 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, D. / Yan, F. / Chen, Y.
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 22, 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

Downloads & links

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Assembly

Deposited unit
A: Something about silencing protein 5
B: Something about silencing protein 5
C: LYS-GLN-LEU-ALA-SER-LYS-ALA-ALA-ARG-LBZ-SER-ALA-PRO-SER-THR-GLY-GLY-VAL-LYS-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2789
Polymers34,7253
Non-polymers5536
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-1 kcal/mol
Surface area15700 Å2
Unit cell
Length a, b, c (Å)126.578, 126.578, 48.708
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Something about silencing protein 5


Mass: 16284.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SAS5, YOR213C / Production host: Escherichia coli (E. coli) / References: UniProt: Q99314
#2: Protein/peptide LYS-GLN-LEU-ALA-SER-LYS-ALA-ALA-ARG-LBZ-SER-ALA-PRO-SER-THR-GLY-GLY-VAL-LYS-TYR


Mass: 2156.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.2M Lithium sulfate, 0.1M Tris-Hcl

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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 22, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 17766 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Χ2: 0.953 / Net I/σ(I): 5.6 / Num. measured all: 118325
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.446.90.8998940.7030.3640.9710.992100
2.44-2.4970.778660.7520.310.8310.98100
2.49-2.536.90.6878800.7870.2790.7431.007100
2.53-2.596.80.588890.8580.2360.6271.012100
2.59-2.646.80.4798640.8970.1970.5190.979100
2.64-2.76.70.4089170.9090.1680.4421.066100
2.7-2.776.50.3268470.9360.1360.3540.99699.9
2.77-2.856.20.2858790.9520.1230.3111.064100
2.85-2.936.40.2328770.9650.0980.2521.061100
2.93-3.026.90.1918920.9810.0770.2061.028100
3.02-3.1370.1578650.9880.0630.171.018100
3.13-3.266.80.1179060.9910.0480.1271.02100
3.26-3.416.80.0978670.9940.0390.1051.026100
3.41-3.586.60.0798890.9950.0330.0851.01100
3.58-3.816.20.0648910.9960.0270.070.964100
3.81-4.16.80.0538950.9980.0220.0580.94299.9
4.1-4.526.90.0438960.9980.0180.0470.856100
4.52-5.176.60.0388860.9990.0160.0420.747100
5.17-6.516.30.0429130.9980.0180.0460.698100
6.51-506.20.0319530.9990.0130.0340.58199.2

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Processing

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

5d7e


Resolution: 2.4→27.4 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 886 5.02 %
Rwork0.227 16779 -
obs0.2294 17665 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.9 Å2 / Biso mean: 67.1069 Å2 / Biso min: 23.14 Å2
Refinement stepCycle: final / Resolution: 2.4→27.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 36 95 2406
Biso mean--72.43 48.68 -
Num. residues----281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.550.35581430.31092734287797
2.55-2.750.33741480.301227562904100
2.75-3.030.30791600.278427822942100
3.03-3.460.28031420.228828012943100
3.46-4.360.22941430.191728282971100
4.36-27.40.26261500.19912878302899
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)
10.1572-1.0723-0.42088.98152.88871.0618-0.4010.56560.13330.61540.3697-1.17280.73411.068-0.01070.98350.1712-0.01121.48170.55461.3202-32.4534.9761-4.3705
23.6142-1.88293.50967.7305-5.30327.6770.22060.51410.55210.1997-1.3729-1.0701-0.14791.82011.08710.70390.06130.01551.08930.23150.9711-37.737211.3-3.708
35.7527-1.72851.68947.7044-3.67875.5862-0.06220.51460.0290.4816-0.4809-0.6239-1.03090.80590.40321.0708-0.0025-0.09890.8090.07970.8343-46.434220.8532-11.4966
44.66751.74015.74323.82531.74517.1293-0.43011.3191.0779-0.4019-0.39940.3555-0.94411.97450.80230.53910.0031-0.01020.60740.15070.615-52.97977.28640.0172
59.1741.2513-1.02082.3446-0.91762.7309-0.4129-0.9194-1.03940.7944-0.2495-0.49991.3319-0.08380.75340.76610.00020.11540.41790.0270.6162-58.7332-1.464618.5407
62.65272.9860.57498.8619-0.14491.7277-0.29560.6825-0.00010.04530.3478-0.9406-0.00480.0582-0.04190.39930.02080.02070.31820.05630.3536-51.11722.880218.1864
71.64440.25662.71775.51793.59226.38080.0151-0.3122-0.92281.1882-0.37132.22791.8306-1.28080.34830.8542-0.18360.20940.43950.10510.5454-68.5738-4.319120.4085
81.7350.07360.46478.7740.61881.60730.0801-0.11090.10790.4271-0.17110.3372-0.0598-0.15130.09210.23590.0110.05380.24370.02850.2498-58.154323.041417.9409
92.7085-0.8251-2.0873.63463.13754.52410.33580.16240.3795-1.0838-0.53951.0911-0.3125-0.53040.12930.35180.0229-0.0720.32150.0290.3001-64.249817.07828.0042
102.0342.32140.45697.29940.7910.9875-0.13040.14170.2669-0.32040.07720.20070.06860.030.07540.21420.01490.00470.19390.01660.2237-59.081616.915211.0316
114.71023.0215-2.6948.0795-2.38696.3299-0.2144-0.0277-0.54460.285-0.3061-0.79130.20080.13490.68440.27660.0018-0.00720.2319-0.00420.2549-53.362514.631714.8722
12-0.05980.2682-0.34637.9509-5.16944.62770.0326-0.07440.11630.6335-0.3311-0.618-0.53870.31780.27490.3158-0.0694-0.06020.36630.0420.3995-49.818933.207715.6861
136.5019-3.8362-0.56989.3927-1.32297.6779-0.3067-0.6487-0.06091.8120.16921.08080.1662-0.07390.14230.68520.0125-0.00250.76670.08070.7326-44.818110.0603-5.1142
141.4703-2.90381.08177.2714-1.93141.07150.61460.0333-0.2774-0.0141-0.6445-0.26940.84350.288-0.0730.97320.16210.00441.17370.29051.0828-39.84522.5269-7.0365
151.86640.0520.06346.1031-2.34312.0904-0.9234-0.6008-0.23960.02840.40412.1917-0.4313-0.20650.53810.75370.18870.04450.85770.12161.1576-52.257611.0742-12.1537
163.1631.92222.36651.29371.47051.82930.13970.4789-0.8452-0.1218-0.3303-0.72540.8034-0.12440.49230.8421-0.00940.08351.36170.42881.2326-36.350713.4153-12.294
171.184-2.34790.40067.5267-1.43012.85220.53180.3102-1.0987-0.38180.3677-0.20141.24680.7689-0.43351.240.4102-0.21441.62160.54941.5801-23.99083.8372-4.3245
185.74221.29463.55079.98061.25292.29810.55240.0934-0.87571.58290.8402-0.86591.31581.2551-1.47261.20.2413-0.16711.51370.34931.0638-33.85099.092-15.4766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 76 through 92 )B76 - 92
2X-RAY DIFFRACTION2chain 'B' and (resid 93 through 111 )B93 - 111
3X-RAY DIFFRACTION3chain 'B' and (resid 112 through 139 )B112 - 139
4X-RAY DIFFRACTION4chain 'C' and (resid 18 through 25 )C18 - 25
5X-RAY DIFFRACTION5chain 'C' and (resid 26 through 37 )C26 - 37
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 17 )A1 - 17
7X-RAY DIFFRACTION7chain 'A' and (resid 18 through 30 )A18 - 30
8X-RAY DIFFRACTION8chain 'A' and (resid 31 through 58 )A31 - 58
9X-RAY DIFFRACTION9chain 'A' and (resid 59 through 75 )A59 - 75
10X-RAY DIFFRACTION10chain 'A' and (resid 76 through 96 )A76 - 96
11X-RAY DIFFRACTION11chain 'A' and (resid 97 through 111 )A97 - 111
12X-RAY DIFFRACTION12chain 'A' and (resid 112 through 139 )A112 - 139
13X-RAY DIFFRACTION13chain 'B' and (resid 4 through 16 )B4 - 16
14X-RAY DIFFRACTION14chain 'B' and (resid 31 through 40 )B31 - 40
15X-RAY DIFFRACTION15chain 'B' and (resid 41 through 48 )B41 - 48
16X-RAY DIFFRACTION16chain 'B' and (resid 49 through 58 )B49 - 58
17X-RAY DIFFRACTION17chain 'B' and (resid 59 through 66 )B59 - 66
18X-RAY DIFFRACTION18chain 'B' and (resid 67 through 75 )B67 - 75

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