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- PDB-7f3s: Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide -

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Basic information

Entry
Database: PDB / ID: 7f3s
TitleCrystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
Components
  • Nuclear protein STH1/NPS1
  • THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LBZ-ALA-PRO-ARG-LYS-GLN-LEU-ALA-SER-TYR
KeywordsNUCLEAR PROTEIN / Histone modification / bromodomain / histone benzoylation / protein-protein interaction
Function / homology
Function and homology information


chromatin remodeling at centromere / DNA translocase activity / nucleosome disassembly / RSC-type complex / ATP-dependent chromatin remodeler activity / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / helicase activity / meiotic cell cycle ...chromatin remodeling at centromere / DNA translocase activity / nucleosome disassembly / RSC-type complex / ATP-dependent chromatin remodeler activity / chromosome, centromeric region / ATP-dependent activity, acting on DNA / cytoskeleton organization / helicase activity / meiotic cell cycle / chromosome segregation / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / base-excision repair / double-strand break repair / DNA helicase / chromatin remodeling / regulation of DNA-templated transcription / chromatin / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain ...Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Nuclear protein STH1/NPS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 17, 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: Nuclear protein STH1/NPS1
B: THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LBZ-ALA-PRO-ARG-LYS-GLN-LEU-ALA-SER-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4553
Polymers15,3632
Non-polymers921
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-8 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.621, 33.206, 42.449
Angle α, β, γ (deg.)88.140, 83.720, 70.480
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nuclear protein STH1/NPS1 / ATP-dependent helicase STH1 / Chromatin structure-remodeling complex protein STH1 / SNF2 homolog


Mass: 13334.953 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: STH1, NPS1, YIL126W / Production host: Escherichia coli (E. coli) / References: UniProt: P32597, DNA helicase
#2: Protein/peptide THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LBZ-ALA-PRO-ARG-LYS-GLN-LEU-ALA-SER-TYR


Mass: 2028.317 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.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 25% (w/v) PEG 1500, 0.1M MIB/Hydrochloric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 4, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 22042 / % possible obs: 92.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 1.142 / Net I/σ(I): 8.1 / Num. measured all: 154912
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.426.20.32110540.9460.1330.3480.62190.2
1.42-1.456.40.30111040.9490.1240.3270.65290.8
1.45-1.486.60.25510910.9660.1030.2760.70592.2
1.48-1.516.80.22610810.9730.0910.2440.77490.5
1.51-1.546.80.20510730.9780.0830.2210.84790.1
1.54-1.586.90.19310440.9770.0780.2080.85186.6
1.58-1.6270.16610630.9850.0660.1790.90190.5
1.62-1.667.30.15711420.9860.0620.1690.93294.7
1.66-1.717.10.14511180.9860.0580.1560.92994
1.71-1.767.10.12711160.9910.050.1371.08493.9
1.76-1.837.20.11411020.990.0460.1231.16193.1
1.83-1.97.10.10610210.9920.0420.1141.32186.2
1.9-1.997.20.09311540.9930.0370.11.29395.4
1.99-2.097.20.08311290.9950.0330.0891.43195.8
2.09-2.227.20.07511420.9950.030.0811.59794.9
2.22-2.397.10.0710690.9950.0280.0751.62889.6
2.39-2.637.40.06311430.9970.0250.0681.5196.1
2.63-3.027.30.05511630.9970.0220.0591.47897.3
3.02-3.87.10.04510900.9990.0180.0491.55292.5
3.8-507.30.03811430.9980.0150.0411.2395.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KMJ

6kmj


Resolution: 1.4→25.19 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.09 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 1175 5.33 %
Rwork0.1637 20857 -
obs0.1647 22032 91.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.45 Å2 / Biso mean: 27.7268 Å2 / Biso min: 14.21 Å2
Refinement stepCycle: final / Resolution: 1.4→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 6 128 1193
Biso mean--49.34 36.16 -
Num. residues----128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.460.24451200.2172479259987
1.46-1.540.23991580.192550270891
1.54-1.630.17811480.17752519266790
1.63-1.760.20991400.18662698283894
1.76-1.940.18951500.17372569271991
1.94-2.220.17041800.16132686286695
2.22-2.790.23291350.17092671280694
2.79-25.190.1521440.14952685282995
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)
16.18385.05334.21025.65845.08567.8518-0.0580.17410.0878-0.10460.03530.0011-0.0880.0748-0.06710.11430.02280.00630.10090.04370.12952.401516.69311.8809
23.0975-0.0851-0.44467.1833-2.24486.4782-0.053-1.0072-0.25260.25980.0211-0.010.12910.51110.07220.15950.02090.00530.37870.08640.23233.7648.427928.5899
37.60551.8118-5.35445.2593-2.19263.9623-0.2395-0.4969-0.30790.05640.00550.14270.8647-0.20960.32410.2207-0.02960.00240.25340.04870.2002-5.16374.894528.9528
44.92386.39496.01249.51636.90938.70490.17950.3118-0.44450.25440.1335-0.35160.32050.4322-0.37080.21760.0250.00140.16870.01050.2149-0.16353.465313.9115
54.4872-3.74032.84163.938-0.5116.47630.32140.3463-0.83350.022-0.26860.00620.8065-0.2703-0.14740.2327-0.0169-0.03480.2023-0.02890.2363-7.0115-0.149610.196
64.77812.6413.03295.37134.37383.77290.0789-0.22560.1037-0.1392-0.11550.0904-0.0376-0.44150.09580.1477-0.00030.00430.16860.02110.1499-9.032511.169220.4699
77.32050.0798-4.95573.5256-0.74423.49370.1888-0.80260.5281.4088-0.1962-0.1168-0.5548-0.27450.09310.31070.0187-0.01250.2893-0.05650.2105-3.609221.60232.2198
86.1661.45214.3691.29261.11573.4162-0.14190.08430.2745-0.0317-0.05380.0111-0.11-0.07180.21920.16410.02640.00480.14230.02480.1676-6.523719.875415.4535
93.34242.1373-1.37345.7425-1.54772.24250.0111-0.89490.53930.0285-0.1915-0.7392-0.48060.45290.21150.25240.0206-0.04220.4651-0.02560.36734.157818.525230.6742
102.88112.01622.07944.51552.56261.91120.1105-0.0485-0.3334-0.1993-0.06120.8530.6364-1.0501-0.00730.3457-0.1004-0.02410.52120.0110.2777-7.21812.043441.0593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1249 through 1275 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1276 through 1289 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1290 through 1299 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1300 through 1308 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1309 through 1314 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1315 through 1332 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1333 through 1337 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1338 through 1358 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 6 through 17 )B6 - 17
10X-RAY DIFFRACTION10chain 'B' and (resid 18 through 23 )B18 - 23

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