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- PDB-5v1a: Structure of S. cerevisiae Ulp2:Csm1 complex -

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Basic information

Entry
Database: PDB / ID: 5v1a
TitleStructure of S. cerevisiae Ulp2:Csm1 complex
Components
  • Monopolin complex subunit CSM1
  • Ubiquitin-like-specific protease 2
KeywordsHYDROLASE / monopolin / rDNA silencing / SUMO isopeptidase / cohibin
Function / homology
Function and homology information


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 / SUMO is proteolytically processed / plasmid maintenance / deSUMOylase activity ...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 / SUMO is proteolytically processed / plasmid maintenance / deSUMOylase activity / rDNA chromatin condensation / protein desumoylation / meiotic sister chromatid cohesion, centromeric / homologous chromosome segregation / attachment of mitotic spindle microtubules to kinetochore / transcription elongation factor activity / chromosome condensation / mitotic spindle assembly checkpoint signaling / Major pathway of rRNA processing in the nucleolus and cytosol / cysteine-type peptidase activity / mitotic spindle / nuclear envelope / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / chromatin / nucleolus / proteolysis / identical protein binding / nucleus
Similarity search - Function
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 / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain ...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 / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / 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
Monopolin complex subunit CSM1 / Ubiquitin-like-specific protease 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 1, 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
B: Ubiquitin-like-specific protease 2
A: Monopolin complex subunit CSM1


Theoretical massNumber of molelcules
Total (without water)17,0322
Polymers17,0322
Non-polymers00
Water36020
1
B: Ubiquitin-like-specific protease 2
A: Monopolin complex subunit CSM1

B: Ubiquitin-like-specific protease 2
A: Monopolin complex subunit CSM1


Theoretical massNumber of molelcules
Total (without water)34,0644
Polymers34,0644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area7090 Å2
ΔGint-51 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.737, 46.737, 124.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein/peptide Ubiquitin-like-specific protease 2


Mass: 2892.225 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: ULP2, SMT4, YIL031W / Production host: Escherichia coli (E. coli) / References: UniProt: P40537, Ulp1 peptidase
#2: Protein Monopolin complex subunit CSM1 / Chromosome segregation in meiosis protein 1


Mass: 14139.714 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM M HEPES pH 7.5 and 20% PEG 3350, 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.14→44 Å / Num. obs: 8129 / % possible obs: 98.7 % / Redundancy: 13.8 % / Rsym value: 0.053 / Net I/σ(I): 53.9
Reflection shellResolution: 2.14→2.2 Å / CC1/2: 0.699 / Rpim(I) all: 0.367 / Rsym value: 1.318

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4S

3n4s


Resolution: 2.14→43.761 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2782 810 10 %
Rwork0.2345 --
obs0.2391 8102 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→43.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms999 0 0 20 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031021
X-RAY DIFFRACTIONf_angle_d0.5651377
X-RAY DIFFRACTIONf_dihedral_angle_d14.216611
X-RAY DIFFRACTIONf_chiral_restr0.039151
X-RAY DIFFRACTIONf_plane_restr0.004172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1399-2.2740.34491280.31461156X-RAY DIFFRACTION98
2.274-2.44960.35011300.29941178X-RAY DIFFRACTION99
2.4496-2.6960.30911320.27751180X-RAY DIFFRACTION99
2.696-3.08610.31721340.25961212X-RAY DIFFRACTION99
3.0861-3.88780.26971380.23051245X-RAY DIFFRACTION100
3.8878-43.77060.25851480.21431321X-RAY DIFFRACTION100
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)
15.63441.17662.14927.17821.45633.19320.1149-0.3183-0.55990.5257-0.03850.13240.1661-0.47550.00170.5219-0.0493-0.01670.5751-0.01380.5161-3.106733.9145-31.9044
21.0768-1.0928-0.0241.08750.01740.083-0.2144-0.5248-0.3228-0.384-0.00450.07560.0192-0.38110.00041.028-0.2155-0.13310.91730.25790.77796.230229.6182-20.5374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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