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- PDB-4jjn: Crystal structure of heterochromatin protein Sir3 in complex with... -

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Basic information

Entry
Database: PDB / ID: 4jjn
TitleCrystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome
Components
  • (DNA (146-MER)) x 2
  • Histone H2A.2
  • Histone H2B.2
  • Histone H3
  • Histone H4
  • Regulatory protein SIR3
KeywordsDNA BINDING PROTEIN/DNA / BAH domain / silencing / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / establishment of protein-containing complex localization to telomere / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / nuclear-transcribed mRNA catabolic process, non-stop decay / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / telomere tethering at nuclear periphery ...sexual sporulation resulting in formation of a cellular spore / establishment of protein-containing complex localization to telomere / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / nuclear-transcribed mRNA catabolic process, non-stop decay / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / telomere tethering at nuclear periphery / 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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA replication checkpoint signaling / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / chromatin silencing complex / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / negative regulation of DNA replication / 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 / DNA replication origin binding / intracellular copper ion homeostasis / DNA replication initiation / Ub-specific processing proteases / subtelomeric heterochromatin formation / heterochromatin / nucleosome binding / CENP-A containing nucleosome / aerobic respiration / double-strand break repair via nonhomologous end joining / structural constituent of chromatin / heterochromatin formation / nucleosome / nucleosome assembly / single-stranded DNA binding / chromatin organization / double-stranded DNA binding / nucleic acid binding / chromosome, telomeric region / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / nucleolus / mitochondrion / DNA binding / identical protein binding / nucleus
Similarity search - Function
: / Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily ...: / Regulatory protein SIR3, C-terminal domain / Bromo adjacent homology (BAH) domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Histone, subunit A / Histone, subunit A / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / SH3 type barrels. / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B.2 / Histone H4 / Histone H2A.2 / Regulatory protein SIR3 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsWang, F. / Li, G. / Mohammed, A. / Lu, C. / Currie, M. / Johnson, A. / Moazed, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Heterochromatin protein Sir3 induces contacts between the amino terminus of histone H4 and nucleosomal DNA.
Authors: Wang, F. / Li, G. / Altaf, M. / Lu, C. / Currie, M.A. / Johnson, A. / Moazed, D.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A.2
D: Histone H2B.2
E: Histone H3
F: Histone H4
G: Histone H2A.2
H: Histone H2B.2
K: Regulatory protein SIR3
L: Regulatory protein SIR3
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)287,13812
Polymers287,13812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.682, 103.682, 556.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3


Mass: 15259.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c
Gene: HHT1, HHT2, Histone H3, N2749, SIN2, YBR010W, YBR0201, YNL031C
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61830
#2: Protein Histone H4


Mass: 11264.194 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c
Gene: HHF1, HHF2, Histone H4, N2752, YBR009C, YBR0122, YNL030W
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02309
#3: Protein Histone H2A.2


Mass: 13881.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: H2A2, Histone H2A.2, HTA2, YBL003C, YBL0103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04912
#4: Protein Histone H2B.2


Mass: 14133.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: H2B2, Histone H2B.2, HTB2, YBL002W, YBL0104 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02294
#5: Protein Regulatory protein SIR3 / Silent information regulator 3


Mass: 43655.582 Da / Num. of mol.: 2 / Mutation: D205N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CMT1, L9753.10, MAR2, SIR3, STE8, YLR442C / Plasmid: pET-Sumo / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P06701

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (146-MER)


Mass: 45138.770 Da / Num. of mol.: 1 / Source method: obtained synthetically
#7: DNA chain DNA (146-MER)


Mass: 45610.043 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.09→139.09 Å / Num. all: 61627 / Num. obs: 60025 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
3.09-3.262.90.4871.50.487197.9
3.26-3.462.80.2572.80.257197.1
3.46-3.6930.1435.10.143199.4
3.69-3.9930.0927.90.092199.3
3.99-4.3730.05512.70.055198
4.37-4.892.90.042170.042196.3
4.89-5.6430.035200.035198.8
5.64-6.912.90.0322.40.03193.3
6.91-9.7730.01827.10.018197.2
9.77-139.092.90.01522.60.015190.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASER(CCP4-6.1.1)phasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→85.45 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 3025 5.07 %random
Rwork0.2313 ---
obs0.2325 59664 97.04 %-
all-61484 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.24 Å2
Refinement stepCycle: LAST / Resolution: 3.09→85.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9635 5986 0 0 15621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216506
X-RAY DIFFRACTIONf_angle_d0.61123533
X-RAY DIFFRACTIONf_dihedral_angle_d21.3166679
X-RAY DIFFRACTIONf_chiral_restr0.0332651
X-RAY DIFFRACTIONf_plane_restr0.0021969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.13910.34271550.3562448X-RAY DIFFRACTION92
3.1391-3.19060.32511230.34252591X-RAY DIFFRACTION99
3.1906-3.24560.38461530.33822637X-RAY DIFFRACTION99
3.2456-3.30460.39571560.32172545X-RAY DIFFRACTION98
3.3046-3.36820.3571380.30712577X-RAY DIFFRACTION97
3.3682-3.4370.28571300.29882575X-RAY DIFFRACTION97
3.437-3.51170.2931450.28342512X-RAY DIFFRACTION97
3.5117-3.59340.31811310.2622694X-RAY DIFFRACTION100
3.5934-3.68320.2931200.25682648X-RAY DIFFRACTION100
3.6832-3.78280.30511370.26652614X-RAY DIFFRACTION99
3.7828-3.89410.31341380.26212655X-RAY DIFFRACTION100
3.8941-4.01980.29371450.25392633X-RAY DIFFRACTION99
4.0198-4.16350.26551280.24462637X-RAY DIFFRACTION98
4.1635-4.33020.291130.23982575X-RAY DIFFRACTION97
4.3302-4.52730.26711420.23572509X-RAY DIFFRACTION94
4.5273-4.76590.26031370.22272538X-RAY DIFFRACTION97
4.7659-5.06450.22991530.2192616X-RAY DIFFRACTION99
5.0645-5.45550.24021520.2322658X-RAY DIFFRACTION99
5.4555-6.00440.27111380.24072556X-RAY DIFFRACTION97
6.0044-6.87290.28391410.24682423X-RAY DIFFRACTION91
6.8729-8.65780.1851320.19262583X-RAY DIFFRACTION97
8.6578-85.4830.16931180.1612415X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 11.8658 Å / Origin y: -20.1545 Å / Origin z: 24.5817 Å
111213212223313233
T0.0328 Å2-0.0438 Å2-0.231 Å2-0.0599 Å2-0.1209 Å2---0.0176 Å2
L0.0257 °20.005 °20.0177 °2-0.0279 °20.0078 °2--0.0969 °2
S0.0621 Å °0.0125 Å °0.059 Å °-0.0027 Å °0.0523 Å °0.0394 Å °-0.0137 Å °-0.0106 Å °0 Å °
Refinement TLS groupSelection details: ALL

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