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- PDB-5v3n: Structure of S. cerevisiae Ulp2-Tof2-Csm1 complex -

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Basic information

Entry
Database: PDB / ID: 5v3n
TitleStructure of S. cerevisiae Ulp2-Tof2-Csm1 complex
Components
  • Monopolin complex subunit CSM1
  • Ulp2p,Topoisomerase 1-associated factor 2 chimera
KeywordsHYDROLASE / monopolin / cohibin / rDNA silencing / desumoylation
Function / homology
Function and homology information


negative regulation of septation initiation signaling / microtubule site clamp / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation ...negative regulation of septation initiation signaling / microtubule site clamp / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic chromosome segregation / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / homologous chromosome segregation / rDNA binding / phosphatase activator activity / rDNA heterochromatin formation / nucleolus organization / attachment of mitotic spindle microtubules to kinetochore / cysteine-type peptidase activity / mitotic spindle / nuclear envelope / nucleolus / mitochondrion / identical protein binding
Similarity search - Function
Nucleolar protein Dnt1-like, N-terminal / Dnt1/Tof2/Net1 / Cdc14 phosphatase binding protein N-terminus / Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain ...Nucleolar protein Dnt1-like, N-terminal / Dnt1/Tof2/Net1 / Cdc14 phosphatase binding protein N-terminus / Aspartate Aminotransferase, domain 1 - #80 / Monopolin complex subunit Csm1/Pcs1, C-terminal / Csm1/Pcs1, C-terminal domain superfamily / Monopolin complex subunit Csm1/Pcs1 / Csm1 N-terminal domain / Chromosome segregation protein Csm1/Pcs1 / Csm1 N-terminal domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Aspartate Aminotransferase, domain 1 / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ulp2p / Monopolin complex subunit CSM1 / Topoisomerase 1-associated factor 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae x Saccharomyces kudriavzevii (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSIngh, N. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM104141 United States
CitationJournal: Genes Dev. / Year: 2017
Title: Recruitment of a SUMO isopeptidase to rDNA stabilizes silencing complexes by opposing SUMO targeted ubiquitin ligase activity.
Authors: Liang, J. / Singh, N. / Carlson, C.R. / Albuquerque, C.P. / Corbett, K.D. / Zhou, H.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Monopolin complex subunit CSM1
B: Ulp2p,Topoisomerase 1-associated factor 2 chimera


Theoretical massNumber of molelcules
Total (without water)17,2612
Polymers17,2612
Non-polymers00
Water1,53185
1
A: Monopolin complex subunit CSM1
B: Ulp2p,Topoisomerase 1-associated factor 2 chimera

A: Monopolin complex subunit CSM1
B: Ulp2p,Topoisomerase 1-associated factor 2 chimera


Theoretical massNumber of molelcules
Total (without water)34,5224
Polymers34,5224
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7890 Å2
ΔGint-39 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.684, 56.933, 40.992
Angle α, β, γ (deg.)90.00, 121.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

21B-118-

HOH

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Components

#1: Protein Monopolin complex subunit CSM1 / Chromosome segregation in meiosis protein 1


Mass: 12991.447 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: CSM1, SPO86, YCR086W, YCR86W / Production host: Escherichia coli (E. coli) / References: UniProt: P25651
#2: Protein/peptide Ulp2p,Topoisomerase 1-associated factor 2 chimera


Mass: 4269.733 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae x Saccharomyces kudriavzevii (yeast), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: VIN7, ATCC 204508 / S288c / Gene: VIN7_2425, TOF2, YKR010C, YK109 / Production host: Escherichia coli (E. coli) / References: UniProt: H0GHZ9, UniProt: Q02208
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium Acetate, 0.1 M HEPES pH 7.5 and 25% PEG 3350 and 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.3→42 Å / Num. obs: 33373 / % possible obs: 96.4 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.042 / Net I/σ(I): 10.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 2.281 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.418 / Rpim(I) all: 1.418 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4S

3n4s


Resolution: 1.3→35.115 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 32.73
RfactorNum. reflection% reflection
Rfree0.2171 3089 4.97 %
Rwork0.192 --
obs0.1934 33323 90.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→35.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 0 85 1221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231182
X-RAY DIFFRACTIONf_angle_d1.7351596
X-RAY DIFFRACTIONf_dihedral_angle_d16.086435
X-RAY DIFFRACTIONf_chiral_restr0.116173
X-RAY DIFFRACTIONf_plane_restr0.013203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.3203104256785
1.3203-1.3420.3987136259090
1.342-1.36510.4348109265288
1.3651-1.38990.3594141274393
1.3899-1.41670.3932150266392
1.4167-1.44560.3564135276993
1.4456-1.4770.3709149273793
1.477-1.51140.2603141269692
1.5114-1.54920.2528135271691
1.5492-1.59110.2556118265889
1.5911-1.63790.1985139279393
1.6379-1.69070.2237136278194
1.6907-1.75120.29371540.1946273194
1.7512-1.82130.2361970.1787270993
1.8213-1.90420.22821630.1621274493
1.9042-2.00450.19741090.1608267991
2.0045-2.13010.20261200.1636280895
2.1301-2.29460.19681300.1577280694
2.2946-2.52540.22611430.17269091
2.5254-2.89070.20191370.184252286
2.8907-3.64140.1861690.1771251986
3.64140.19541740.1799249986

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