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- PDB-6mje: Structure of Candida glabrata Csm1: S. cerevisiae Dsn1 complex -

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Basic information

Entry
Database: PDB / ID: 6mje
TitleStructure of Candida glabrata Csm1: S. cerevisiae Dsn1 complex
Components
  • Dsn1p
  • Monopolin complex subunit CSM1
KeywordsCELL CYCLE / monopolin / kinetochore
Function / homology
Function and homology information


microtubule site clamp / MIS12/MIND type complex / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / rDNA chromatin condensation / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion, centromeric ...microtubule site clamp / MIS12/MIND type complex / chromosome, centromeric core domain / monopolin complex / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / rDNA chromatin condensation / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion, centromeric / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / Neutrophil degranulation / chromosome segregation / kinetochore / spindle pole / mitotic spindle / nuclear envelope / cell division / nucleolus / 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 / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / Aspartate Aminotransferase, domain 1 ...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 / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / Aspartate Aminotransferase, domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Monopolin complex subunit CSM1 / Dsn1p / Kinetochore-associated protein DSN1 / Candida glabrata strain CBS138 chromosome E complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Chromosoma / Year: 2019
Title: The molecular basis of monopolin recruitment to the kinetochore.
Authors: Plowman, R. / Singh, N. / Tromer, E.C. / Payan, A. / Duro, E. / Spanos, C. / Rappsilber, J. / Snel, B. / Kops, G.J.P.L. / Corbett, K.D. / Marston, A.L.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2019Group: 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 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Monopolin complex subunit CSM1
B: Dsn1p
C: Monopolin complex subunit CSM1
D: Dsn1p
E: Monopolin complex subunit CSM1
F: Dsn1p
G: Monopolin complex subunit CSM1
H: Dsn1p


Theoretical massNumber of molelcules
Total (without water)81,3408
Polymers81,3408
Non-polymers00
Water00
1
A: Monopolin complex subunit CSM1
B: Dsn1p
G: Monopolin complex subunit CSM1
H: Dsn1p


Theoretical massNumber of molelcules
Total (without water)40,6704
Polymers40,6704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-45 kcal/mol
Surface area14890 Å2
MethodPISA
2
C: Monopolin complex subunit CSM1
D: Dsn1p
E: Monopolin complex subunit CSM1
F: Dsn1p


Theoretical massNumber of molelcules
Total (without water)40,6704
Polymers40,6704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-43 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.368, 203.755, 44.259
Angle α, β, γ (deg.)90.00, 90.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Monopolin complex subunit CSM1


Mass: 15571.603 Da / Num. of mol.: 4 / Fragment: UNP residues 69-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: AO440_000897, AO440_004693 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0CH22, UniProt: Q6FVN3*PLUS
#2: Protein/peptide
Dsn1p


Mass: 4763.462 Da / Num. of mol.: 4 / Fragment: UNP residues 71-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DSN1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L4A9Z4, UniProt: P40568*PLUS

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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: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25% PEG3350, cryoprotect with additional 20% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.127 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26122 / % possible obs: 96 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.091 / Rrim(I) all: 0.219 / Net I/σ(I): 18.2
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.793 / Num. unique obs: 1446 / Rpim(I) all: 0.488 / Rrim(I) all: 0.938

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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: PDB entry 3N4R

3n4r


Resolution: 2.5→43.351 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 43.07
RfactorNum. reflection% reflection
Rfree0.2972 1277 4.98 %
Rwork0.2397 --
obs0.2426 25661 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 0 0 4561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074641
X-RAY DIFFRACTIONf_angle_d0.8916234
X-RAY DIFFRACTIONf_dihedral_angle_d15.9242800
X-RAY DIFFRACTIONf_chiral_restr0.047690
X-RAY DIFFRACTIONf_plane_restr0.005791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4946-2.59450.48821150.3972175X-RAY DIFFRACTION75
2.5945-2.71250.4781290.39022527X-RAY DIFFRACTION89
2.7125-2.85550.41221620.34932648X-RAY DIFFRACTION93
2.8555-3.03440.41371560.34152763X-RAY DIFFRACTION97
3.0344-3.26860.35141380.27392817X-RAY DIFFRACTION97
3.2686-3.59740.3541320.23632849X-RAY DIFFRACTION99
3.5974-4.11760.28191360.23362880X-RAY DIFFRACTION99
4.1176-5.18640.21351740.18382833X-RAY DIFFRACTION100
5.1864-43.35780.2771350.21512892X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.1476 Å / Origin y: -24.6765 Å / Origin z: 4.351 Å
111213212223313233
T0.6159 Å20.0032 Å2-0.0029 Å2-0.5882 Å20.0268 Å2--0.5472 Å2
L0.1558 °2-0.3193 °2-0.1494 °2-2.614 °20.9115 °2--0.4058 °2
S-0.0612 Å °0.0025 Å °0.0117 Å °0.0906 Å °0.0401 Å °-0.0421 Å °0.0171 Å °0.0258 Å °0 Å °
Refinement TLS groupSelection details: all

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