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- PDB-6qsz: Crystal structure of the Sir4 H-BRCT domain in complex with Esc1 ... -

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Basic information

Entry
Database: PDB / ID: 6qsz
TitleCrystal structure of the Sir4 H-BRCT domain in complex with Esc1 pS1450 peptide
Components
  • Regulatory protein SIR4
  • Silent chromatin protein ESC1
KeywordsNUCLEAR PROTEIN / Heterochromatin
Function / homology
Function and homology information


: / chromosome, telomeric region => GO:0000781 / subtelomeric heterochromatin formation => GO:0031509 / establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding ...: / chromosome, telomeric region => GO:0000781 / subtelomeric heterochromatin formation => GO:0031509 / establishment of protein-containing complex localization to telomere / telomere tethering at nuclear periphery / chromatin silencing complex / silent mating-type cassette heterochromatin formation / positive regulation of heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin formation / nuclear periphery / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / chromosome, telomeric region / molecular adaptor activity
Similarity search - Function
Sir4, SID domain / Sir4 SID domain / Leucine-rich repeat profile. / Leucine-rich repeat
Similarity search - Domain/homology
Regulatory protein SIR4 / Silent chromatin protein ESC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDeshpande, I. / Keusch, J.J. / Challa, K. / Iesmantavicius, V. / Gasser, S.M. / Gut, H.
CitationJournal: Embo J. / Year: 2019
Title: The Sir4 H-BRCT domain interacts with phospho-proteins to sequester and repress yeast heterochromatin.
Authors: Deshpande, I. / Keusch, J.J. / Challa, K. / Iesmantavicius, V. / Gasser, S.M. / Gut, H.
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein SIR4
B: Silent chromatin protein ESC1
C: Regulatory protein SIR4
D: Silent chromatin protein ESC1
E: Regulatory protein SIR4
F: Silent chromatin protein ESC1
G: Regulatory protein SIR4
H: Silent chromatin protein ESC1
I: Regulatory protein SIR4
J: Silent chromatin protein ESC1
K: Regulatory protein SIR4
L: Silent chromatin protein ESC1
M: Regulatory protein SIR4
N: Silent chromatin protein ESC1
O: Regulatory protein SIR4
P: Silent chromatin protein ESC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,97417
Polymers134,93816
Non-polymers351
Water3,279182
1
A: Regulatory protein SIR4
B: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area7320 Å2
MethodPISA
2
C: Regulatory protein SIR4
D: Silent chromatin protein ESC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9033
Polymers16,8672
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-12 kcal/mol
Surface area7500 Å2
MethodPISA
3
E: Regulatory protein SIR4
F: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area7360 Å2
MethodPISA
4
G: Regulatory protein SIR4
H: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area7560 Å2
MethodPISA
5
K: Regulatory protein SIR4
L: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-5 kcal/mol
Surface area7460 Å2
MethodPISA
6
M: Regulatory protein SIR4
N: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area7440 Å2
MethodPISA
7
O: Regulatory protein SIR4
P: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5 kcal/mol
Surface area7290 Å2
MethodPISA
8
I: Regulatory protein SIR4
J: Silent chromatin protein ESC1


Theoretical massNumber of molelcules
Total (without water)16,8672
Polymers16,8672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6 kcal/mol
Surface area7120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.060, 68.340, 77.810
Angle α, β, γ (deg.)72.61, 84.10, 87.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Regulatory protein SIR4 / Silent information regulator 4


Mass: 15059.491 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: fragment, residues 961-1085
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P11978
#2: Protein/peptide
Silent chromatin protein ESC1 / Establishes silent chromatin protein 1


Mass: 1807.777 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: fragment of Q03661, residues 1443-1458
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q03661
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000 0.2 M ammonium acetate 0.1 m sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42465 / % possible obs: 96.4 % / Redundancy: 2 % / Biso Wilson estimate: 67 Å2 / CC1/2: 0.995 / Rsym value: 0.091 / Net I/σ(I): 7.69
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 2 % / CC1/2: 0.291 / % possible all: 92.5

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.58 Å / Cor.coef. Fo:Fc: 0.9367 / Cor.coef. Fo:Fc free: 0.9137 / SU R Cruickshank DPI: 0.447 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.249 / SU Rfree Cruickshank DPI: 0.26
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 2124 5 %RANDOM
Rwork0.1893 ---
obs0.1916 42465 96.53 %-
Displacement parametersBiso mean: 71.93 Å2
Baniso -1Baniso -2Baniso -3
1-5.2056 Å2-0.3485 Å2-6.7382 Å2
2---16.3449 Å2-3.4567 Å2
3---11.1393 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: 1 / Resolution: 2.5→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7999 0 1 182 8182
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018229HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1411077HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2982SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes262HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1104HARMONIC5
X-RAY DIFFRACTIONt_it8229HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion20.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1070SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8990SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3141 149 5.01 %
Rwork0.251 2823 -
all0.2541 2972 -
obs--96.53 %
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)
16.4392-0.8408-0.12131.4646-0.05235.115-0.0561-0.03080.0335-0.066-0.0836-0.0279-0.17460.00880.1397-0.20040.0389-0.0449-0.0892-0.0356-0.09316.0194-8.40885.4389
20.43760.1069-1.47234.1521.68939.6379-0.07590.195-0.4194-0.36450.1026-0.28890.6216-0.0077-0.0267-0.0743-0.03960.1434-0.1499-0.0082-0.15141.825116.454439.4262
33.8713-0.7962-1.72271.2831-0.11016.2903-0.0913-0.42840.06930.2690.0227-0.1917-0.13110.76560.0686-0.1239-0.0304-0.07630.02250.0003-0.2234-21.872-5.039232.5985
43.7911-2.048-2.71851.17040.41937.7606-0.17910.6911-0.21930.0138-0.26170.17830.3447-0.77730.4407-0.1175-0.07690.02570.0037-0.1188-0.2134-44.3435-9.707249.0775
54.9613-0.4589-0.47210.73230.34393.9071-0.01570.4728-0.2319-0.14990.03220.1121-0.086-0.3325-0.0165-0.1541-0.008-0.0564-0.00750.0057-0.093-28.3186-9.71396.0189
61.6305-0.1176-1.36434.5925-2.15124.91560.041-0.1870.07890.43890.08040.4636-0.0264-0.2524-0.1214-0.0573-0.01830.116-0.069-0.0777-0.1741.4261-33.734918.5341
73.51452.6111-0.39723.1454-1.26596.1959-0.22960.11220.3319-0.02640.0801-0.0514-0.67380.02030.1495-0.07170.105-0.0286-0.13190.0939-0.1516-12.71756.903-10.8066
82.3910.3379-2.20053.5516-1.35057.3884-0.1056-0.0403-0.1601-0.3883-0.2875-0.46711.10920.57930.3931-0.02310.17980.1304-0.15170.0885-0.1762-44.2551-41.59790.5837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ O|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ E|* }
5X-RAY DIFFRACTION5{ G|* }
6X-RAY DIFFRACTION6{ I|* }
7X-RAY DIFFRACTION7{ K|* }
8X-RAY DIFFRACTION8{ M|* }

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