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- PDB-5t6j: Structure of the MIND Complex Shows a Regulatory Focus of Yeast K... -

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Basic information

Entry
Database: PDB / ID: 5t6j
TitleStructure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly
Components
  • Kinetochore protein SPC24
  • Kinetochore protein SPC25
  • Kinetochore-associated protein DSN1
KeywordsCELL CYCLE / kinetochore / complex / chromosome / segregation / MIND / Mis12 / Mtw1 / Spc24 / Spc25 / Ndc80 / Nuf2
Function / homology
Function and homology information


MIS12/MIND type complex / centromere clustering / Ndc80 complex / spindle attachment to meiosis I kinetochore / sister chromatid biorientation / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion, centromeric / outer kinetochore / Neutrophil degranulation / chromosome segregation ...MIS12/MIND type complex / centromere clustering / Ndc80 complex / spindle attachment to meiosis I kinetochore / sister chromatid biorientation / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion, centromeric / outer kinetochore / Neutrophil degranulation / chromosome segregation / kinetochore / spindle pole / cell division / identical protein binding / nucleus
Similarity search - Function
Double Stranded RNA Binding Domain - #430 / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / Double Stranded RNA Binding Domain / EF-Hand 1, calcium-binding site ...Double Stranded RNA Binding Domain - #430 / Chromosome segregation protein Spc25 / Spc24, Fungi, globular domain superfamily / Kinetochore-associated protein Dsn1/Mis13 / Mis12-Mtw1 protein family / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / Double Stranded RNA Binding Domain / EF-Hand 1, calcium-binding site / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinetochore protein SPC25 / Kinetochore-associated protein DSN1 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å
AuthorsValverde, R. / Jenni, S. / Dimitrova, Y. / Khin, Y. / Harrison, S.C.
CitationJournal: Cell / Year: 2016
Title: Structure of the MIND Complex Defines a Regulatory Focus for Yeast Kinetochore Assembly.
Authors: Dimitrova, Y.N. / Jenni, S. / Valverde, R. / Khin, Y. / Harrison, S.C.
History
DepositionSep 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Kinetochore protein SPC24
B: Kinetochore protein SPC25
C: Kinetochore-associated protein DSN1


Theoretical massNumber of molelcules
Total (without water)18,4243
Polymers18,4243
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-35 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.889, 85.889, 95.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Kinetochore protein SPC24


Mass: 6942.951 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: SPC24, YMR117C, YM9718.16C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04477
#2: Protein Kinetochore protein SPC25


Mass: 10030.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues S130, N131, A132 are left over from the TEV protease cleavage site.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SPC25, YER018C / Production host: Escherichia coli (E. coli) / References: UniProt: P40014
#3: Protein/peptide Kinetochore-associated protein DSN1


Mass: 1450.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DSN1, YIR010W, YIB10W / Production host: Escherichia coli (E. coli) / References: UniProt: P40568
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.0-7.5, 1.0 M potassium sodium tartrate, 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.999965 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999965 Å / Relative weight: 1
ReflectionResolution: 1.75→42.944 Å / Num. obs: 18161 / % possible obs: 100 % / Redundancy: 17.6 % / Net I/σ(I): 25.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FTX

2ftx


Resolution: 1.752→42.944 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 880 4.85 %
Rwork0.2241 --
obs0.225 18160 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.752→42.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 73 1359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061305
X-RAY DIFFRACTIONf_angle_d0.7931766
X-RAY DIFFRACTIONf_dihedral_angle_d13.579788
X-RAY DIFFRACTIONf_chiral_restr0.044206
X-RAY DIFFRACTIONf_plane_restr0.005228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7517-1.86150.35381380.33812802X-RAY DIFFRACTION99
1.8615-2.00520.31411540.28972820X-RAY DIFFRACTION100
2.0052-2.2070.27871490.24962859X-RAY DIFFRACTION100
2.207-2.52630.28181390.23312868X-RAY DIFFRACTION100
2.5263-3.18280.24171380.22622909X-RAY DIFFRACTION100
3.1828-42.95740.20811620.19983022X-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)
12.50453.09360.80953.85750.95672.94740.0546-0.16641.34870.579-0.43310.3955-0.90860.1708-1.18630.4763-0.0622-0.11060.22250.07690.4138-6.979320.6333-25.6057
23.8451-1.2665-1.29512.6141-0.61982.50220.49531.01470.1351-0.0297-1.1183-0.61480.17630.5796-1.41660.2755-0.05630.01140.42160.34590.31896.894214.1837-33.9313
30.09160.1022-0.28052.60530.89611.9474-0.13440.10570.22940.0004-0.153-1.1052-0.02540.8904-0.29830.2343-0.0706-0.10310.23620.07980.34638.80818.8845-24.2768
41.9659-0.04061.0781.76010.26811.23320.1304-0.22720.48260.2369-0.18720.1260.0318-0.73680.00070.2812-0.0223-0.0230.3108-0.01220.2973-7.976514.218-21.4698
55.1436-0.49671.85772.72272.75933.97830.1316-0.8266-0.6740.51140.3469-0.25551.4987-1.17210.47020.6604-0.2094-0.02130.4146-0.03020.4064-3.96798.9712-12.4607
60.1797-0.02850.11280.3261-0.42150.57840.1804-0.35580.24710.4470.48030.185-0.1662-0.1280.02881.34520.5072-0.2041.1968-0.62271.1554-7.680227.5586-6.631
70.07280.0699-0.04240.09970.01030.07890.3635-0.35011.07120.50670.33760.4377-0.4279-0.48320.00060.78-0.01640.25910.6206-0.12990.58-4.472320.3185-4.3887
80.0669-0.00170.00490.0460.010.0627-0.13630.1747-0.06480.6070.4707-0.14970.2683-0.3654-0.0010.8893-0.2936-0.05540.54970.01140.34660.31510.7537-3.6585
93.0822-0.83520.94840.548-0.79441.3324-0.3306-0.19630.71030.47510.3974-0.6686-0.61930.7850.15670.5238-0.0755-0.07540.3439-0.12430.32145.302223.4264-7.406
100.5548-0.443-0.07260.39680.03850.28280.03330.2789-0.04030.34570.6675-0.67980.39460.66830.25980.35730.0534-0.14080.2523-0.080.31554.90313.2274-12.4155
110.04530.02-0.03580.10150.02490.12190.59880.39930.8206-0.25650.1524-0.8635-0.35650.62720.00110.83330.14240.01240.8173-0.24370.9878-10.015625.9459-17.1255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 155 through 168 )
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 199 )
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 213 )
4X-RAY DIFFRACTION4chain 'B' and (resid 130 through 163 )
5X-RAY DIFFRACTION5chain 'B' and (resid 164 through 173 )
6X-RAY DIFFRACTION6chain 'B' and (resid 174 through 178 )
7X-RAY DIFFRACTION7chain 'B' and (resid 179 through 183 )
8X-RAY DIFFRACTION8chain 'B' and (resid 184 through 189 )
9X-RAY DIFFRACTION9chain 'B' and (resid 190 through 205 )
10X-RAY DIFFRACTION10chain 'B' and (resid 206 through 221 )
11X-RAY DIFFRACTION11chain 'C' and (resid 560 through 571 )

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