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- PDB-6mjb: Structure of Candida glabrata Csm1:Dsn1(14-72) complex -

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Basic information

Entry
Database: PDB / ID: 6mjb
TitleStructure of Candida glabrata Csm1:Dsn1(14-72) complex
Components
  • Kinetochore-associated protein DSN1
  • 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 / meiotic sister chromatid cohesion, centromeric / attachment of mitotic spindle microtubules to kinetochore ...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 / meiotic sister chromatid cohesion, centromeric / attachment of mitotic spindle microtubules to kinetochore / chromosome segregation / 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 / 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: 2.27 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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Kinetochore-associated protein DSN1


Theoretical massNumber of molelcules
Total (without water)33,6913
Polymers33,6913
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-36 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.632, 71.632, 122.258
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Monopolin complex subunit CSM1


Mass: 13513.335 Da / Num. of mol.: 2 / Fragment: UNP residues 69-181 / Mutation: N-terminal tag scar SNA
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 Kinetochore-associated protein DSN1


Mass: 6664.171 Da / Num. of mol.: 1 / Fragment: UNP residues 14-72
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.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.45 M ammonium sulfate, 5% PEG3350, 0.1 M Bis-Tris, pH 5.5, cryoprotectant: 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2014
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.27→122 Å / Num. obs: 16495 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.053 / Rrim(I) all: 0.128 / Net I/σ(I): 14.3
Reflection shellResolution: 2.27→2.39 Å / Rmerge(I) obs: 1.125 / Num. unique obs: 2420 / Rpim(I) all: 0.52 / Rrim(I) all: 1.241

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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: 2.27→43.542 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.245 832 5.07 %
Rwork0.1954 --
obs0.1978 16438 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.27→43.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 0 112 2188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072116
X-RAY DIFFRACTIONf_angle_d0.8632847
X-RAY DIFFRACTIONf_dihedral_angle_d14.2931281
X-RAY DIFFRACTIONf_chiral_restr0.048315
X-RAY DIFFRACTIONf_plane_restr0.004362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2701-2.33690.3461520.31132541X-RAY DIFFRACTION100
2.3369-2.41240.34831510.28612567X-RAY DIFFRACTION100
2.4124-2.49860.32521520.27362532X-RAY DIFFRACTION99
2.4986-2.59860.29691280.26572575X-RAY DIFFRACTION100
2.5986-2.71680.28011320.2542580X-RAY DIFFRACTION100
2.7168-2.86010.28121340.2362548X-RAY DIFFRACTION100
2.8601-3.03920.30711350.21762539X-RAY DIFFRACTION100
3.0392-3.27380.24031420.19772576X-RAY DIFFRACTION100
3.2738-3.60310.25991250.17072544X-RAY DIFFRACTION100
3.6031-4.12410.1941360.15592568X-RAY DIFFRACTION100
4.1241-5.19460.18271230.13992541X-RAY DIFFRACTION99
5.1946-43.54960.20971270.18932553X-RAY DIFFRACTION99
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)
11.0319-0.7893-1.20924.06560.74983.17080.17430.0725-0.0025-0.0202-0.0651-0.2481-0.21550.0540.00070.42610.0140.01620.3424-0.00230.372272.833963.71193.7661
21.9658-0.2108-0.72181.9151-0.14514.2826-0.04590.12820.0165-0.02170.05540.12510.0109-0.34270.00050.4253-0.047-0.00160.2942-0.01450.379274.494951.6415-13.854
31.40060.15950.66721.3403-0.42240.65770.1362-0.09320.1482-0.175-0.09090.2271-0.1215-0.2368-0.0020.50960.06130.03860.4248-0.0090.424860.416858.833614.6091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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