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- PDB-6rr0: Crystal structure of the Sir4 H-BRCT domain in complex with Ubp10... -

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Basic information

Entry
Database: PDB / ID: 6rr0
TitleCrystal structure of the Sir4 H-BRCT domain in complex with Ubp10 pT123 peptide
Components
  • Regulatory protein SIR4
  • Ubiquitin carboxyl-terminal hydrolase 10
KeywordsNUCLEAR PROTEIN / heterochromatin
Function / homology
Function and homology information


: / 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 / protein deubiquitination / nuclear replication fork ...: / 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 / protein deubiquitination / nuclear replication fork / subtelomeric heterochromatin formation / nucleosome binding / heterochromatin formation / double-strand break repair via nonhomologous end joining / ubiquitin-dependent protein catabolic process / double-stranded DNA binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / chromosome, telomeric region / molecular adaptor activity / cysteine-type endopeptidase activity / nucleolus / nucleus / cytosol
Similarity search - Function
Sir4, SID domain / Sir4 SID domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Regulatory protein SIR4 / Ubiquitin carboxyl-terminal hydrolase 10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionMay 16, 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: Regulatory protein SIR4
C: Regulatory protein SIR4
D: Regulatory protein SIR4
E: Regulatory protein SIR4
F: Regulatory protein SIR4
G: Regulatory protein SIR4
H: Ubiquitin carboxyl-terminal hydrolase 10
I: Ubiquitin carboxyl-terminal hydrolase 10
J: Ubiquitin carboxyl-terminal hydrolase 10
K: Ubiquitin carboxyl-terminal hydrolase 10
L: Ubiquitin carboxyl-terminal hydrolase 10
M: Ubiquitin carboxyl-terminal hydrolase 10
N: Ubiquitin carboxyl-terminal hydrolase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,46516
Polymers113,39414
Non-polymers712
Water5,711317
1
A: Regulatory protein SIR4
H: Ubiquitin carboxyl-terminal hydrolase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2704
Polymers16,1992
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-30 kcal/mol
Surface area7350 Å2
MethodPISA
2
B: Regulatory protein SIR4
I: Ubiquitin carboxyl-terminal hydrolase 10


Theoretical massNumber of molelcules
Total (without water)16,1992
Polymers16,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-8 kcal/mol
Surface area7820 Å2
MethodPISA
3
C: Regulatory protein SIR4
L: Ubiquitin carboxyl-terminal hydrolase 10


Theoretical massNumber of molelcules
Total (without water)16,1992
Polymers16,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area7620 Å2
MethodPISA
4
D: Regulatory protein SIR4
K: Ubiquitin carboxyl-terminal hydrolase 10


Theoretical massNumber of molelcules
Total (without water)16,1992
Polymers16,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-6 kcal/mol
Surface area7150 Å2
MethodPISA
5
E: Regulatory protein SIR4
J: Ubiquitin carboxyl-terminal hydrolase 10


Theoretical massNumber of molelcules
Total (without water)16,1992
Polymers16,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-7 kcal/mol
Surface area7230 Å2
MethodPISA
6
F: Regulatory protein SIR4
M: Ubiquitin carboxyl-terminal hydrolase 10


Theoretical massNumber of molelcules
Total (without water)16,1992
Polymers16,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-8 kcal/mol
Surface area7320 Å2
MethodPISA
7
G: Regulatory protein SIR4
N: Ubiquitin carboxyl-terminal hydrolase 10


Theoretical massNumber of molelcules
Total (without water)16,1992
Polymers16,1992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-7 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.040, 75.280, 95.910
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14871.911 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: Fragment (residues 961-1085)
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIR4, ASD1, STE9, UTH2, YDR227W, YD9934.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21 DE3 STAR / References: UniProt: P11978
#2: Protein/peptide
Ubiquitin carboxyl-terminal hydrolase 10 / Deubiquitinating enzyme 10 / Disrupter of telomere silencing protein 4 / Ubiquitin thioesterase 10 ...Deubiquitinating enzyme 10 / Disrupter of telomere silencing protein 4 / Ubiquitin thioesterase 10 / Ubiquitin-specific-processing protease 10


Mass: 1327.287 Da / Num. of mol.: 7 / Source method: obtained synthetically / Details: Fragment (residues 117-128)
Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53874, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 27.8 % PEG 4000 0.1 M sodium acetate pH 4.9 0.2 M ammonium acetate 3% w/v trimethylamine N-oxide dehydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 51736 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.27 Å2 / CC1/2: 0.998 / Rsym value: 0.14 / Net I/σ(I): 9.51
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 3797 / CC1/2: 0.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→47.57 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9295 / SU R Cruickshank DPI: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.248 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2587 5 %RANDOM
Rwork0.1963 ---
obs0.1975 51735 99.9 %-
Displacement parametersBiso mean: 57.25 Å2
Baniso -1Baniso -2Baniso -3
1-2.5186 Å20 Å28.6016 Å2
2--1.6545 Å20 Å2
3----4.1732 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: 1 / Resolution: 2.18→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7131 0 2 317 7450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017339HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.059880HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2684SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes232HARMONIC2
X-RAY DIFFRACTIONt_gen_planes988HARMONIC5
X-RAY DIFFRACTIONt_it7339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion18.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion965SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8002SEMIHARMONIC4
LS refinement shellResolution: 2.18→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2426 189 4.99 %
Rwork0.2224 3601 -
all0.2234 3790 -
obs--99.9 %
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)
12.84880.27331.85451.14951.25853.8140.0275-0.3240.06410.0524-0.14790.1413-0.0119-0.32390.1204-0.1775-0.0257-0.0107-0.1376-0.0121-0.11535.8887-1.5587.8321
23.0242-0.96961.11911.92120.29271.0560.21790.2995-0.3138-0.1026-0.0658-0.08250.08250.1785-0.1522-0.07240.0108-0.0447-0.07680.0009-0.051430.5625-14.169412.0637
32.61030.25731.49761.4095-0.61861.6926-0.0458-0.1068-0.07620.03140.08610.1485-0.0579-0.189-0.0403-0.06410.03430.0054-0.05940.0015-0.05438.9086-9.1891-18.8356
43.89650.56671.96773.42850.83041.73040.0025-0.07330.1530.11610.0293-0.2247-0.00130.0706-0.0318-0.1091-0.0374-0.0371-0.11070.0236-0.053946.78641.193729.7128
55.02520.45051.33981.2389-0.46292.9257-0.04830.52620.0374-0.1426-0.0434-0.174-0.06080.29790.0917-0.11730.0075-0.0163-0.05470.0187-0.1034-2.8603-7.4267-17.6773
64.78021.44712.46924.5898-0.33293.0109-0.34350.33270.3945-0.60190.14730.2539-0.1530.04470.1962-0.0725-0.0169-0.0681-0.17640.0586-0.148829.545-1.3149-44.0679
77.17171.31745.15193.5904-0.35854.10090.5984-0.6098-0.7840.112-0.0933-0.08440.4773-0.3012-0.5051-0.1421-0.0516-0.1783-0.1870.0936-0.07825.7323-14.5748-50.0537
80.7575-3.75623.82115.1994-3.11313.4461-0.05040.04220.3462-0.016-0.03250.2098-0.2603-0.33760.083-0.19310.0676-0.02230.1415-0.2030.033-7.18211.2954.5576
96.02223.8753.5617.93713.07660.80760.08780.0769-0.3574-0.2411-0.18710.20750.2929-0.16320.09920.09180.1724-0.2007-0.0946-0.1556-0.049523.1011-18.68031.2871
103.7891-1.68193.71232.84575.19493.7491-0.00070.2184-0.1241-0.20350.06350.17750.13120.0213-0.0628-0.09670.03430.03070.20490.0291-0.1287-9.2538-7.6243-30.9173
112.30633.89354.39164.58362.60174.5079-0.03090.26080.1508-0.1897-0.05780.1589-0.0464-0.05340.0887-0.05260.0277-0.0513-0.04070.010.072735.22727.887423.4372
126.9561-2.533-1.01181.15294.48885.2160.0342-0.1680.00580.19050.02560.2965-0.0878-0.2849-0.0598-0.0887-0.0136-0.02510.06920.0436-0.040125.2953-13.0896-22.5538
133.20663.17250.54350.36951.12085.189-0.09130.35540.0989-0.1363-0.02930.10820.15260.00690.1207-0.0081-0.1931-0.3214-0.05760.23290.049822.04532.6451-55.1874
142.36990.16983.4080.5226-2.76673.59420.0056-0.1693-0.16280.0290.01750.21520.2003-0.2427-0.02310.0668-0.127-0.3307-0.27680.09280.1964-5.5133-22.4497-57.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|970 - A|1084 }
2X-RAY DIFFRACTION2{ B|967 - B|1085 }
3X-RAY DIFFRACTION3{ C|968 - C|1084 }
4X-RAY DIFFRACTION4{ D|970 - D|1084 }
5X-RAY DIFFRACTION5{ E|970 - E|1085 }
6X-RAY DIFFRACTION6{ F|969 - F|1084 }
7X-RAY DIFFRACTION7{ G|970 - G|1084 }
8X-RAY DIFFRACTION8{ H|117 - H|127 }
9X-RAY DIFFRACTION9{ I|117 - I|127 }
10X-RAY DIFFRACTION10{ J|117 - J|127 }
11X-RAY DIFFRACTION11{ K|117 - K|127 }
12X-RAY DIFFRACTION12{ L|117 - L|128 }
13X-RAY DIFFRACTION13{ M|117 - M|127 }
14X-RAY DIFFRACTION14{ N|117 - N|127 }

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