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- PDB-6dei: Structure of Dse3-Csm1 complex -

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Basic information

Entry
Database: PDB / ID: 6dei
TitleStructure of Dse3-Csm1 complex
Components
  • Monopolin complex subunit CSM1
  • Protein DSE3
KeywordsProtein Binding/Cell Cycle / monopolin / daughter cell-specific protein / Protein Binding-Cell Cycle complex
Function / homology
Function and homology information


monopolin complex / 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 / cellular bud neck / nuclear envelope / cell cycle ...monopolin complex / 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 / cellular bud neck / nuclear envelope / cell cycle / nucleolus / identical protein binding / nucleus / cytoplasm
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 / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Monopolin complex subunit CSM1 / Protein DSE3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 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)R01GM104141 United States
CitationJournal: Protein Sci. / Year: 2018
Title: The budding-yeast RWD protein Csm1 scaffolds diverse protein complexes through a conserved structural mechanism.
Authors: Singh, N. / Corbett, K.D.
History
DepositionMay 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: entity / pdbx_related_exp_data_set
Item: _entity.formula_weight / _pdbx_related_exp_data_set.data_reference
Revision 1.3Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Monopolin complex subunit CSM1
B: Monopolin complex subunit CSM1
C: Protein DSE3
D: Protein DSE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7537
Polymers31,3934
Non-polymers3593
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.442, 51.235, 117.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12991.447 Da / Num. of mol.: 2
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 Protein DSE3 / Daughter specific expression protein 3


Mass: 2705.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DSE3, YOR264W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08729
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaOAc, 0.1M HEPES pH 7.5, 22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.99833 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99833 Å / Relative weight: 1
ReflectionResolution: 1.699→39.3 Å / Num. obs: 28421 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 8.3
Reflection shellResolution: 1.699→1.73 Å / Num. unique all: 1451 / CC1/2: 0.436 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N4S

3n4s


Resolution: 1.699→39.095 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1999 7.06 %
Rwork0.1887 --
obs0.1911 28297 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→39.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 24 232 2312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072127
X-RAY DIFFRACTIONf_angle_d0.7632859
X-RAY DIFFRACTIONf_dihedral_angle_d13.6061271
X-RAY DIFFRACTIONf_chiral_restr0.047313
X-RAY DIFFRACTIONf_plane_restr0.004356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6992-1.74170.36551360.35141785X-RAY DIFFRACTION97
1.7417-1.78880.34551400.30751844X-RAY DIFFRACTION99
1.7888-1.84140.2861410.27851854X-RAY DIFFRACTION99
1.8414-1.90090.28421420.24671861X-RAY DIFFRACTION100
1.9009-1.96880.25291400.2151842X-RAY DIFFRACTION100
1.9688-2.04760.22291410.20141864X-RAY DIFFRACTION100
2.0476-2.14080.24581420.19651863X-RAY DIFFRACTION100
2.1408-2.25370.23641410.1841861X-RAY DIFFRACTION100
2.2537-2.39490.25231410.16651870X-RAY DIFFRACTION100
2.3949-2.57970.25281450.17231896X-RAY DIFFRACTION100
2.5797-2.83930.21851440.18541889X-RAY DIFFRACTION99
2.8393-3.24990.2121440.16761903X-RAY DIFFRACTION100
3.2499-4.09390.19581480.15391935X-RAY DIFFRACTION100
4.0939-39.10550.16481540.18092031X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -7.7943 Å / Origin y: 1.2655 Å / Origin z: 11.6193 Å
111213212223313233
T0.1179 Å20.0154 Å20.0128 Å2-0.1133 Å20.0117 Å2--0.1348 Å2
L0.8204 °20.5082 °20.2254 °2-0.9377 °20.3468 °2--0.7095 °2
S0.0048 Å °-0.11 Å °-0.0372 Å °0.1104 Å °-0.0285 Å °-0.034 Å °0.03 Å °0.0349 Å °0.0378 Å °
Refinement TLS groupSelection details: all

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