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- PDB-6mjc: Structure of Candida glabrata Csm1:Dsn1(43-67DD) complex -

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Basic information

Entry
Database: PDB / ID: 6mjc
TitleStructure of Candida glabrata Csm1:Dsn1(43-67DD) complex
Components
  • Kinetochore-associated protein DSN1
  • Monopolin complex subunit CSM1
KeywordsCELL CYCLE / monopolin / kinetochore
Function / homology
Function and homology information


MIS12/MIND type complex / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / mitotic sister chromatid segregation / spindle pole / nuclear envelope / cell division ...MIS12/MIND type complex / monopolin complex / spindle attachment to meiosis I kinetochore / protein localization to nucleolar rDNA repeats / meiotic sister chromatid cohesion, centromeric / rDNA chromatin condensation / mitotic sister chromatid segregation / spindle pole / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Monopolin complex subunit CSM1 / Kinetochore-associated protein DSN1 / Candida glabrata strain CBS138 chromosome L complete sequence / Candida glabrata strain CBS138 chromosome E complete sequence
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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: Kinetochore-associated protein DSN1


Theoretical massNumber of molelcules
Total (without water)16,7452
Polymers16,7452
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.057, 105.057, 125.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Monopolin complex subunit CSM1


Mass: 13513.335 Da / Num. of mol.: 1 / 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 Kinetochore-associated protein DSN1


Mass: 3231.515 Da / Num. of mol.: 1 / Fragment: UNP residues 43-67 / Mutation: S66D, S67D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0L09603g, AO440_005223, AO440_005782 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W0D923, UniProt: Q6FKQ5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 3 M sodium chloride, cryoprotectant: 0.5 M sodium chloride, 0.5 M sodium malonate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 22, 2018
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→75 Å / Num. obs: 25112 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.016 / Rrim(I) all: 0.034 / Net I/σ(I): 20
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 1.44 / Num. unique obs: 1462 / Rpim(I) all: 0.753 / Rrim(I) all: 1.025

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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: 1.79→52.529 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.01
RfactorNum. reflection% reflection
Rfree0.2232 1198 4.77 %
Rwork0.1991 --
obs0.2001 25097 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.79→52.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 0 59 1139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121099
X-RAY DIFFRACTIONf_angle_d1.181480
X-RAY DIFFRACTIONf_dihedral_angle_d15.994665
X-RAY DIFFRACTIONf_chiral_restr0.061166
X-RAY DIFFRACTIONf_plane_restr0.007189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7901-1.86170.32961170.34012623X-RAY DIFFRACTION99
1.8617-1.94650.30061200.29272668X-RAY DIFFRACTION100
1.9465-2.04910.2511450.25532619X-RAY DIFFRACTION100
2.0491-2.17750.26071340.23892637X-RAY DIFFRACTION100
2.1775-2.34560.22021500.21682626X-RAY DIFFRACTION100
2.3456-2.58160.25731250.23152658X-RAY DIFFRACTION100
2.5816-2.95520.26571530.23162646X-RAY DIFFRACTION100
2.9552-3.72310.21321390.1982664X-RAY DIFFRACTION99
3.7231-52.55110.19021150.16592758X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -13.1902 Å / Origin y: 48.7233 Å / Origin z: 6.238 Å
111213212223313233
T0.3494 Å2-0.0573 Å2-0.0796 Å2-0.371 Å2-0.0161 Å2--0.3517 Å2
L4.0464 °2-0.0994 °20.4602 °2-2.8317 °21.0931 °2--3.2677 °2
S-0.0353 Å °0.2534 Å °-0.188 Å °-0.2573 Å °-0.0032 Å °0.3058 Å °0.1349 Å °-0.1864 Å °0.0613 Å °
Refinement TLS groupSelection details: all

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