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- PDB-6kmj: Crystal structure of Sth1 bromodomain in complex with H3K14Ac -

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Basic information

Entry
Database: PDB / ID: 6kmj
TitleCrystal structure of Sth1 bromodomain in complex with H3K14Ac
Components
  • Histone H3
  • Nuclear protein STH1/NPS1
KeywordsGENE REGULATION / Chromatin remodeling / histone acetylation / RSC complex / Sth1 / bromodomain
Function / homology
Function and homology information


: / 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 / DNA translocase activity ...: / 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 / DNA translocase activity / nucleosome array spacer activity / Oxidative Stress Induced Senescence / RSC-type complex / ATP-dependent chromatin remodeler activity / nucleosome disassembly / 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 / histone H4 reader activity / chromosome, centromeric region / intracellular copper ion homeostasis / CENP-A containing nucleosome / : / cytoskeleton organization / aerobic respiration / meiotic cell cycle / chromosome segregation / transcription elongation by RNA polymerase II / helicase activity / base-excision repair / structural constituent of chromatin / nucleosome / double-strand break repair / chromatin organization / DNA helicase / chromatin remodeling / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / 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, chromatin remodelling complex / Snf2, ATP coupling domain / 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 / Bromodomain-like / Histone Acetyltransferase; Chain A / Helicase conserved C-terminal domain / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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 / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Nuclear protein STH1/NPS1 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChen, G. / Li, W. / Yan, F. / Wang, D. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670748 China
CitationJournal: Structure / Year: 2020
Title: The Structural Basis for Specific Recognition of H3K14 Acetylation by Sth1 in the RSC Chromatin Remodeling Complex.
Authors: Chen, G. / Li, W. / Yan, F. / Wang, D. / Chen, Y.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear protein STH1/NPS1
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3063
Polymers15,2142
Non-polymers921
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, Sth1 (chain A) and H3 (chain B) form 1:1 complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-9 kcal/mol
Surface area7640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.943, 61.933, 153.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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 BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P32597, DNA helicase
#2: Protein/peptide Histone H3


Mass: 1879.169 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P61830
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES sodium pH 7.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 21820 / % possible obs: 94.3 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.052 / Rrim(I) all: 0.146 / Χ2: 2.08 / Net I/σ(I): 5.5 / Num. measured all: 179344
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.429.10.66310210.8610.2210.7010.67392.4
1.42-1.458.90.59810850.8880.2020.6320.75895
1.45-1.489.10.5210490.8880.1750.550.8492.5
1.48-1.518.90.44110560.9180.1490.4670.96890.6
1.51-1.549.10.41210290.910.1410.4371.03894
1.54-1.5880.38310670.9120.1390.4091.13991.6
1.58-1.629.10.34110220.9460.1160.3611.28592.5
1.62-1.668.90.33210740.9420.1140.3521.32792.7
1.66-1.7190.29410400.9550.0990.3111.56390.3
1.71-1.768.70.2710560.9580.0940.2871.72492.6
1.76-1.838.20.2410490.9690.0850.2552.04690.3
1.83-1.97.80.22110380.9670.0820.2372.25692.9
1.9-1.998.20.19510950.9780.0690.2082.50892.9
1.99-2.0980.17810920.9810.0650.192.89695.6
2.09-2.227.50.15311270.9810.0570.1643.24296
2.22-2.396.80.13711330.9770.0560.1493.49496.3
2.39-2.637.60.13211350.9880.0510.1423.54899
2.63-3.027.40.11711950.9880.0460.1263.55699.6
3.02-3.87.10.10211670.990.0420.113.81899.2
3.8-507.60.09312900.9940.0360.13.89699.2

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GRC

2grc


Resolution: 1.4→28.708 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 1110 5.1 %
Rwork0.1647 20654 -
obs0.166 21764 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 19.7242 Å2 / Biso min: 8.12 Å2
Refinement stepCycle: final / Resolution: 1.4→28.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1067 0 6 129 1202
Biso mean--28.13 34.28 -
Num. residues----129
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4001-1.46380.23411190.1951248593
1.4638-1.54090.21671330.1738249492
1.5409-1.63750.20851400.1644249993
1.6375-1.76390.20581390.1632247591
1.7639-1.94140.20691110.1649252192
1.9414-2.22220.1791620.1598259495
2.2222-2.79930.18431460.1649270998
2.7993-28.70.17741600.1627287799
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)
12.80940.71471.19341.95990.93734.0156-0.17670.5929-0.2427-0.20240.1608-0.00590.12220.156-0.03230.1332-0.02380.01160.1959-0.04390.1204-1.7313-17.915-32.8253
21.32260.3735-0.49061.5368-0.53151.8122-0.039-0.04510.0277-0.0195-0.0278-0.1601-0.02370.12790.07530.1062-0.0128-0.01010.1139-0.00330.11513.5679-12.3594-17.2217
32.0121-0.0965-0.63372.0483-0.24490.9175-0.1715-0.339-0.30190.13910.03830.20540.3989-0.10920.16020.1646-0.01770.03430.18420.04150.1675-5.9703-23.2032-9.6493
41.23310.016-0.16141.44091.12783.2376-0.02030.0873-0.0496-0.011-0.05560.06250.1508-0.25620.05380.0979-0.0137-0.0040.09310.010.1012-7.7767-19.2048-21.0519
51.28260.47611.2980.59580.58023.7135-0.02540.12850.1362-0.1253-0.01570.0589-0.2068-0.18060.10620.13750.0143-0.00940.14020.02240.1322-8.34-8.5754-25.0451
61.42160.4084-0.05240.6053-0.23150.09560.0166-0.03090.1763-0.0557-0.0780.0163-0.05590.06560.05220.13830.0034-0.01180.14110.00420.15923.2754-9.2337-8.9567
73.2271-0.4462.13411.9723-0.86274.83220.2148-0.35670.1174-0.04340.0069-0.05520.2664-0.0646-0.10950.15660.01480.00880.16230.01240.1442-4.6399-14.6272.2865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1248 through 1263 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1264 through 1287 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1288 through 1299 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1300 through 1337 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1338 through 1359 )A0
6X-RAY DIFFRACTION6chain 'C' and (resid 6 through 17 )C6 - 17
7X-RAY DIFFRACTION7chain 'C' and (resid 18 through 22 )C18 - 22

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