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- PDB-1q1a: Structure of the yeast Hst2 protein deacetylase in ternary comple... -

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Basic information

Entry
Database: PDB / ID: 1q1a
TitleStructure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide
Components
  • HST2 protein
  • Histone H4
KeywordsGENE REGULATION / ternary complex / histone deacetylase / 2'-O-ADP ribose
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / HATs acetylate histones / histone H4K16 deacetylase activity, NAD-dependent / 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 / HDACs deacetylate histones ...Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / HATs acetylate histones / histone H4K16 deacetylase activity, NAD-dependent / 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 / HDACs deacetylate histones / protein acetyllysine N-acetyltransferase / rDNA heterochromatin formation / histone deacetylase activity, NAD-dependent / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / 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 / NAD+ binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / metal ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE / Histone H4 / NAD-dependent protein deacetylase HST2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhao, K. / Chai, X. / Marmorstein, R.
Citation
Journal: Structure / Year: 2003
Title: Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-Acetyl ADP ribose and histone peptide.
Authors: Zhao, K. / Chai, X. / Marmorstein, R.
#1: Journal: Nat.Struct.Biol. / Year: 2003
Title: Structure and autoregulation of the yeast Hst2 homolog of Sir2
Authors: Zhao, K. / Chai, X. / Clements, A. / Marmorstein, R.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HST2 protein
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5194
Polymers33,8522
Non-polymers6672
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.421, 98.421, 77.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsprotein is a monomer upon the substrate binding

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Components

#1: Protein HST2 protein / Homologous to SIR2 protein 2


Mass: 32654.424 Da / Num. of mol.: 1 / Fragment: C-terminla deletion of hst2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P53686
#2: Protein/peptide Histone H4


Mass: 1197.457 Da / Num. of mol.: 1 / Fragment: Residues 12-21 / Source method: obtained synthetically / Details: chemically synthesized / References: UniProt: P02309
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OAD / 2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE


Type: RNA linking / Mass: 601.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N5O15P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4K, , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
20.2 M1reservoirNH4(OAc)
3100 mMsodium citrate1reservoirpH5.6
425 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2003
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 43331 / Num. obs: 42619 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.045 / Net I/σ(I): 20.9
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4192 / Rsym value: 0.163 / % possible all: 93.9
Reflection
*PLUS
Num. obs: 43331
Reflection shell
*PLUS
% possible obs: 93.9 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q14

1q14


Resolution: 1.5→29.74 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2130 5 %RANDOM
Rwork0.183 ---
all0.203 43331 --
obs0.183 42619 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5557 Å2 / ksol: 0.385886 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å21.04 Å20 Å2
2--1.14 Å20 Å2
3----2.27 Å2
Refine analyzeLuzzati coordinate error free: 0.18 Å / Luzzati sigma a free: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2355 0 40 303 2698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.742
X-RAY DIFFRACTIONc_scangle_it4.162.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 305 4.6 %
Rwork0.214 6290 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4AADPR
Refinement
*PLUS
Highest resolution: 1.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.231 / Rfactor Rwork: 0.218

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