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- PDB-7f4e: Crystal structure of Hst2 in complex with H3K9bz peptide -

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Basic information

Entry
Database: PDB / ID: 7f4e
TitleCrystal structure of Hst2 in complex with H3K9bz peptide
Components
  • Histone H3
  • NAD-dependent protein deacetylase HST2
KeywordsNUCLEAR PROTEIN / histone modification / histone benzoylation / protein-protein interaction / NAD-dependent histone deacetylase
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / histone H4K16 deacetylase activity, NAD-dependent / 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 ...Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / histone H4K16 deacetylase activity, NAD-dependent / 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 / protein acetyllysine N-acetyltransferase / rDNA heterochromatin formation / histone deacetylase activity, NAD-dependent / Oxidative Stress Induced Senescence / 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 / NAD+ binding / intracellular copper ion homeostasis / CENP-A containing nucleosome / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. ...Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / 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
NAD-dependent protein deacetylase HST2 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 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

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase HST2
C: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7283
Polymers33,6632
Non-polymers651
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-3 kcal/mol
Surface area13370 Å2
Unit cell
Length a, b, c (Å)42.150, 68.402, 94.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NAD-dependent protein deacetylase HST2 / Homologous to SIR2 protein 2 / Regulatory protein SIR2 homolog 2


Mass: 32523.293 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: HST2, YPL015C, LPA2C / Production host: Escherichia coli (E. coli)
References: UniProt: P53686, protein acetyllysine N-acetyltransferase
#2: Protein/peptide Histone H3


Mass: 1139.263 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P61830
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% (w/v) PEG 1500, 0.1M MMT/Sodium hydroxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97855 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 26704 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Χ2: 0.959 / Net I/σ(I): 6.7 / Num. measured all: 167194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.814.50.80212030.6360.3990.9010.98189.9
1.81-1.845.30.74712600.7190.3480.8280.9995.3
1.84-1.885.80.69213000.7810.3110.760.98698.9
1.88-1.926.20.55613550.8860.2420.6080.97799.6
1.92-1.966.50.4712920.9230.1990.5120.99299.7
1.96-26.50.39213390.9370.1670.4260.98499.7
2-2.0560.29813090.9590.1310.3261.00199.5
2.05-2.116.50.2513440.9710.1060.2721.02699.9
2.11-2.176.80.23113230.9780.0960.251.01499.9
2.17-2.246.80.17213230.9860.0710.1870.9999.9
2.24-2.326.60.14213370.990.0590.1540.96899.7
2.32-2.426.50.12313370.9920.0520.1340.94599.8
2.42-2.5360.10213430.9920.0450.1110.94899.8
2.53-2.666.80.08413380.9960.0350.0910.93399.7
2.66-2.836.70.07113570.9970.0290.0770.94199.9
2.83-3.046.60.05913490.9970.0250.0640.88799.7
3.04-3.356.10.04813600.9970.0210.0520.89199.3
3.35-3.836.80.04113730.9980.0170.0440.8999.6
3.83-4.836.20.03713790.9980.0160.040.88499.3
4.83-506.10.04214830.9970.0190.0460.98598.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1A

1q1a


Resolution: 1.78→28.61 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1215 4.82 %
Rwork0.1838 23978 -
obs0.1853 25193 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.45 Å2 / Biso mean: 32.0897 Å2 / Biso min: 7.52 Å2
Refinement stepCycle: final / Resolution: 1.78→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 1 234 2528
Biso mean--30.83 36.49 -
Num. residues----287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.850.2799940.24161739183362
1.85-1.940.29831260.23532347247385
1.94-2.040.28391380.21012721285997
2.04-2.170.23151490.186427972946100
2.17-2.330.22141430.187528232966100
2.33-2.570.23941390.190328272966100
2.57-2.940.2471300.185428652995100
2.94-3.70.18531470.17622864301199
3.7-28.610.17621490.16492995314499
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)
11.27310.71490.42981.9760.48612.86680.05320.46350.0484-0.4287-0.03480.10320.0488-0.1167-0.06210.16380.0238-0.03070.2293-0.0330.1128-13.95231.7726-38.406
21.8705-1.5678-3.1354.11441.50135.509-0.5555-0.3888-0.96760.7253-0.09410.13721.31120.91740.28690.4320.22350.08470.6455-0.05150.77576.6664-6.2014-16.175
33.218-2.5956-1.81752.28670.48877.5817-0.3165-0.7194-0.7066-0.01330.21230.17690.70560.1861-0.04110.28060.01250.03410.24870.04380.17511.82340.2897-6.2763
41.1646-0.35692.06660.6072-0.88473.941-0.4220.26270.25620.2937-0.16490.14010.15250.9283-0.49260.23730.01310.09330.3177-0.03120.22638.49424.7315-20.4245
50.97240.24190.3721.91830.46761.73720.0281-0.02440.06940.21540.1307-0.1587-0.19370.22580.05430.1135-0.0260.01630.1302-0.0350.14730.042211.4478-19.0948
62.14650.4168-0.0992.56610.23322.17570.00620.1734-0.0119-0.0689-0.00380.21870.071-0.1466-0.02120.07490.0034-0.00970.1074-0.02490.1361-15.27182.1966-31.8908
75.0669-0.94342.75570.2497-0.25872.5350.2972-0.8923-0.30890.5138-0.1610.3617-0.481-0.8942-0.21250.7182-0.12960.05950.4180.0450.2789-12.77132.0655-11.1839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 39 )A8 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 62 )A40 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 76 )A63 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 94 )A77 - 94
5X-RAY DIFFRACTION5chain 'A' and (resid 95 through 189 )A95 - 189
6X-RAY DIFFRACTION6chain 'A' and (resid 190 through 293 )A190 - 293
7X-RAY DIFFRACTION7chain 'C' and (resid 6 through 14 )C6 - 14

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